7-20701025-A-G

Variant names:

• chr7-20701025-A-G
• rs17218211
• NM_001163941.2:c.2337+890A>G

Variant summary

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

The NM_001163941.2(ABCB5):​c.2337+890A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,186 control chromosomes in the GnomAD database, including 3,062 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 0.19 (3062 hom., cov: 32)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.2337+890A>G		intron_variant	Intron 19 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.1002+890A>G		intron_variant	Intron 10 of 18		NP_848654.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.2337+890A>G		intron_variant	Intron 19 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.1002+890A>G		intron_variant	Intron 10 of 18	1		ENSP00000258738.6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29229 AN: 152068 Hom.: 3057 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.192 AC: 29252 AN: 152186 Hom.: 3062 Cov.: 32 AF XY: 0.188 AC XY: 13994 AN XY: 74404

African (AFR) AF: 0.142 AC: 5906 AN: 41518

American (AMR) AF: 0.248 AC: 3789 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3466

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5186

South Asian (SAS) AF: 0.149 AC: 717 AN: 4814

European-Finnish (FIN) AF: 0.142 AC: 1501 AN: 10598

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15895 AN: 67996

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.224 Hom.: 8517

Bravo AF: 0.197

Asia WGS AF: 0.0940 AC: 328 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	1.8
DANN	Benign	0.29
PhyloP100		-0.57
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: rs17218211; hg19: chr7-20740648;