NM_001163941.2:c.1536+614C>A

Variant names:

• chr7-20652237-C-A
• rs17816709
• NM_001163941.2:c.1536+614C>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.1536+614C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,024 control chromosomes in the GnomAD database, including 2,307 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 0.16 (2307 hom., cov: 32)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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.1536+614C>A		intron	N/A	NP_001157413.1
	ABCB5	NM_178559.6		c.201+614C>A		intron	N/A	NP_848654.3
	ABCB5	NM_001163942.2		c.201+614C>A		intron	N/A	NP_001157414.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	ENST00000404938.7	TSL:1 MANE Select	c.1536+614C>A		intron	N/A	ENSP00000384881.2
	ABCB5	ENST00000258738.10	TSL:1	c.201+614C>A		intron	N/A	ENSP00000258738.6
	ABCB5	ENST00000443026.6	TSL:1	c.201+614C>A		intron	N/A	ENSP00000406730.2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23932 AN: 151906 Hom.: 2305 Cov.: 32

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.157 AC: 23935 AN: 152024 Hom.: 2307 Cov.: 32 AF XY: 0.162 AC XY: 12000 AN XY: 74278

African (AFR) AF: 0.0549 AC: 2278 AN: 41502

American (AMR) AF: 0.127 AC: 1939 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3470

East Asian (EAS) AF: 0.0353 AC: 183 AN: 5186

South Asian (SAS) AF: 0.193 AC: 929 AN: 4804

European-Finnish (FIN) AF: 0.303 AC: 3180 AN: 10498

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14153 AN: 67978

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.173 Hom.: 1136

Bravo AF: 0.138

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.086
DANN	Benign	0.57
PhyloP100		-2.4
Mutation Taster		=99/1	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: rs17816709; hg19: chr7-20691860;