7-20628654-C-A

Variant names:

• chr7-20628654-C-A
• rs78414512
• NM_001163941.2:c.109-34C>A

Variant summary

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

The NM_001163941.2(ABCB5):​c.109-34C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,590,304 control chromosomes in the GnomAD database, including 16,061 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 0.11 (1208 hom., cov: 32)
  • Exomes 𝑓: 0.14 (14853 hom.)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 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.109-34C>A		intron	N/A	NP_001157413.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	ENST00000404938.7	TSL:1 MANE Select	c.109-34C>A		intron	N/A	ENSP00000384881.2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16516 AN: 151010 Hom.: 1208 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0981

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.000788

Gnomad SAS AF: 0.0608

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.0976

GnomAD2 exomes AF: 0.113 AC: 25715 AN: 226808 AF XY: 0.116

Gnomad AFR exome AF: 0.0214

Gnomad AMR exome AF: 0.0624

Gnomad ASJ exome AF: 0.124

Gnomad EAS exome AF: 0.00191

Gnomad FIN exome AF: 0.223

Gnomad NFE exome AF: 0.150

Gnomad OTH exome AF: 0.124

GnomAD4 exome AF: 0.137 AC: 197309 AN: 1439172 Hom.: 14853 Cov.: 31 AF XY: 0.136 AC XY: 96967 AN XY: 713988

African (AFR) AF: 0.0187 AC: 621 AN: 33148

American (AMR) AF: 0.0661 AC: 2773 AN: 41950

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 3245 AN: 25620

East Asian (EAS) AF: 0.00108 AC: 42 AN: 39066

South Asian (SAS) AF: 0.0704 AC: 5881 AN: 83500

European-Finnish (FIN) AF: 0.222 AC: 11578 AN: 52184

Middle Eastern (MID) AF: 0.107 AC: 600 AN: 5622

European-Non Finnish (NFE) AF: 0.150 AC: 165085 AN: 1098618

Other (OTH) AF: 0.126 AC: 7484 AN: 59464

GnomAD4 genome AF: 0.109 AC: 16515 AN: 151132 Hom.: 1208 Cov.: 32 AF XY: 0.111 AC XY: 8199 AN XY: 73832

African (AFR) AF: 0.0259 AC: 1066 AN: 41236

American (AMR) AF: 0.0979 AC: 1482 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3452

East Asian (EAS) AF: 0.000790 AC: 4 AN: 5062

South Asian (SAS) AF: 0.0612 AC: 292 AN: 4768

European-Finnish (FIN) AF: 0.225 AC: 2363 AN: 10480

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.155 AC: 10477 AN: 67704

Other (OTH) AF: 0.0966 AC: 202 AN: 2092

Alfa AF: 0.133 Hom.: 300

Bravo AF: 0.0950

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.050
DANN	Benign	0.52
PhyloP100		-3.1
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: rs78414512; hg19: chr7-20668277;