rs6958596

Variant names:

• chr7-20655112-C-T
• rs6958596
• NM_001163941.2:c.1537-3394C>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.1537-3394C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 150,414 control chromosomes in the GnomAD database, including 2,424 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 0.18 (2424 hom., cov: 30)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.1537-3394C>T		intron_variant	Intron 13 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.202-3394C>T		intron_variant	Intron 4 of 18		NP_848654.3
ABCB5	NM_001163942.2	c.202-3394C>T		intron_variant	Intron 4 of 5		NP_001157414.1
ABCB5	NM_001163993.3	c.202-3394C>T		intron_variant	Intron 4 of 5		NP_001157465.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.1537-3394C>T		intron_variant	Intron 13 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.202-3394C>T		intron_variant	Intron 4 of 18	1		ENSP00000258738.6
ABCB5	ENST00000443026.6	c.202-3394C>T		intron_variant	Intron 4 of 5	1		ENSP00000406730.2
ABCB5	ENST00000406935.5	c.202-3394C>T		intron_variant	Intron 4 of 5	2		ENSP00000383899.1

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26648 AN: 150314 Hom.: 2421 Cov.: 30

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0650

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.177 AC: 26675 AN: 150414 Hom.: 2424 Cov.: 30 AF XY: 0.179 AC XY: 13090 AN XY: 73286

African (AFR) AF: 0.208 AC: 8507 AN: 40934

American (AMR) AF: 0.173 AC: 2625 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 621 AN: 3458

East Asian (EAS) AF: 0.197 AC: 1006 AN: 5104

South Asian (SAS) AF: 0.212 AC: 1011 AN: 4780

European-Finnish (FIN) AF: 0.161 AC: 1605 AN: 9954

Middle Eastern (MID) AF: 0.128 AC: 37 AN: 290

European-Non Finnish (NFE) AF: 0.160 AC: 10868 AN: 67744

Other (OTH) AF: 0.160 AC: 336 AN: 2094

Alfa AF: 0.162 Hom.: 3424

Bravo AF: 0.178

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.21
PhyloP100		0.14
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: rs6958596; hg19: chr7-20694735;