chr6-43432099-A-G

Position:

• chr6-43432099-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ABCC10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC10	NM_001198934.2	c.162-43A>G		intron_variant		ENST00000372530.9	NP_001185863.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC10	ENST00000372530.9	c.162-43A>G		intron_variant		2	NM_001198934.2	ENSP00000361608.4

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

GnomAD3 exomes AF: 0.876 AC: 211057 AN: 240980 Hom.: 92704 AF XY: 0.879 AC XY: 114166 AN XY: 129888

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 SAS exome AF: 0.900

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

Gnomad4 AFR exome AF: 0.871

Gnomad4 AMR exome AF: 0.791

Gnomad4 ASJ exome AF: 0.868

Gnomad4 EAS exome AF: 0.936

Gnomad4 SAS exome AF: 0.895

Gnomad4 FIN exome AF: 0.873

Gnomad4 NFE exome AF: 0.892

Gnomad4 OTH exome AF: 0.879

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

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.868

Alfa AF: 0.885 Hom.: 123832

Bravo AF: 0.871

Asia WGS AF: 0.921 AC: 3203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.63
BranchPoint Hunter		2.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs700008; hg19: chr6-43399837;