rs700008

Variant names:

• chr6-43432099-A-G
• rs700008
• ENST00000244533.7:c.-11A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-43432099-A-G
• chr6-43432099-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033450.3(ABCC10):​c.-11A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 1,599,254 control chromosomes in the GnomAD database, including 629,577 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.88 (58584 hom., cov: 31)
  • Exomes 𝑓: 0.89 (570993 hom.)
• Consequence: ABCC10 NM_033450.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890
• Publications: 13 publications found

Genes affected

ABCC10 (HGNC:52): (ATP binding cassette subfamily C member 10) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This ABC full-transporter is a member of the MRP subfamily which is involved in multi-drug resistance. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033450.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC10	NM_001198934.2	MANE Select	c.162-43A>G		intron	N/A	NP_001185863.1	Q5T3U5-1
	ABCC10	NM_033450.3		c.-11A>G		5_prime_UTR	Exon 1 of 20	NP_258261.2
	ABCC10	NM_001350518.2		c.-78-1136A>G		intron	N/A	NP_001337447.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC10	ENST00000244533.7	TSL:1	c.-11A>G		5_prime_UTR	Exon 1 of 20	ENSP00000244533.3	Q5T3U5-2
	ABCC10	ENST00000372530.9	TSL:2 MANE Select	c.162-43A>G		intron	N/A	ENSP00000361608.4	Q5T3U5-1
	ABCC10	ENST00000921385.1		c.162-43A>G		intron	N/A	ENSP00000591444.1

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133337 AN: 152066 Hom.: 58553 Cov.: 31

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.869

GnomAD2 exomes AF: 0.876 AC: 211057 AN: 240980 AF XY: 0.879

Gnomad AFR exome AF: 0.867

Gnomad AMR exome AF: 0.787

Gnomad ASJ exome AF: 0.863

Gnomad EAS exome AF: 0.950

Gnomad FIN exome AF: 0.873

Gnomad NFE exome AF: 0.888

Gnomad OTH exome AF: 0.863

GnomAD4 exome AF: 0.888 AC: 1284824 AN: 1447070 Hom.: 570993 Cov.: 65 AF XY: 0.888 AC XY: 637785 AN XY: 718042

African (AFR) AF: 0.871 AC: 28950 AN: 33236

American (AMR) AF: 0.791 AC: 34562 AN: 43694

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 21672 AN: 24956

East Asian (EAS) AF: 0.936 AC: 36994 AN: 39506

South Asian (SAS) AF: 0.895 AC: 75483 AN: 84382

European-Finnish (FIN) AF: 0.873 AC: 46105 AN: 52816

Middle Eastern (MID) AF: 0.832 AC: 4736 AN: 5694

European-Non Finnish (NFE) AF: 0.892 AC: 983777 AN: 1103036

Other (OTH) AF: 0.879 AC: 52545 AN: 59750

GnomAD4 genome AF: 0.877 AC: 133415 AN: 152184 Hom.: 58584 Cov.: 31 AF XY: 0.876 AC XY: 65185 AN XY: 74400

African (AFR) AF: 0.867 AC: 35981 AN: 41502

American (AMR) AF: 0.832 AC: 12724 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2978 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4916 AN: 5176

South Asian (SAS) AF: 0.904 AC: 4358 AN: 4822

European-Finnish (FIN) AF: 0.871 AC: 9233 AN: 10598

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60313 AN: 68004

Other (OTH) AF: 0.868 AC: 1836 AN: 2114

Alfa AF: 0.886 Hom.: 267482

Bravo AF: 0.871

Asia WGS AF: 0.921 AC: 3203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.63
PhyloP100		0.89
BranchPoint Hunter		2.0
PromoterAI		-0.031	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs700008; hg19: chr6-43399837;