7-20692397-C-T

Variant names:

• chr7-20692397-C-T
• rs2190409
• NM_001163941.2:c.2011-6010C>T

Variant summary

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

The NM_001163941.2(ABCB5):​c.2011-6010C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 151,576 control chromosomes in the GnomAD database, including 51,962 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 0.83 (51962 hom., cov: 29)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 1 publications found

Genes affected

ABCB5 (HGNC:46): (ATP binding cassette subfamily B member 5) ABCB5 belongs to the ATP-binding cassette (ABC) transporter superfamily of integral membrane proteins. These proteins participate in ATP-dependent transmembrane transport of structurally diverse molecules ranging from small ions, sugars, and peptides to more complex organic molecules (Chen et al., 2005 [PubMed 15760339]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001163941.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	NM_001163941.2	MANE Select	c.2011-6010C>T		intron	N/A	NP_001157413.1
	ABCB5	NM_178559.6		c.676-6010C>T		intron	N/A	NP_848654.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	ENST00000404938.7	TSL:1 MANE Select	c.2011-6010C>T		intron	N/A	ENSP00000384881.2
	ABCB5	ENST00000258738.10	TSL:1	c.676-6010C>T		intron	N/A	ENSP00000258738.6

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125251 AN: 151460 Hom.: 51921 Cov.: 29

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.843

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.827 AC: 125353 AN: 151576 Hom.: 51962 Cov.: 29 AF XY: 0.831 AC XY: 61546 AN XY: 74028

African (AFR) AF: 0.778 AC: 32125 AN: 41292

American (AMR) AF: 0.876 AC: 13337 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2949 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4561 AN: 5158

South Asian (SAS) AF: 0.890 AC: 4277 AN: 4804

European-Finnish (FIN) AF: 0.847 AC: 8864 AN: 10464

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.832 AC: 56457 AN: 67862

Other (OTH) AF: 0.845 AC: 1777 AN: 2104

Alfa AF: 0.830 Hom.: 6142

Bravo AF: 0.826

Asia WGS AF: 0.888 AC: 3079 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.40
PhyloP100		-0.076
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2190409; hg19: chr7-20732020;