NM_001163941.2:c.2867+716T>C

Variant names:

• chr7-20729171-T-C
• rs4719626
• NM_001163941.2:c.2867+716T>C

Variant summary

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

The NM_001163941.2(ABCB5):​c.2867+716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,052 control chromosomes in the GnomAD database, including 10,553 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 0.36 (10553 hom., cov: 32)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.2867+716T>C		intron_variant	Intron 23 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.1532+716T>C		intron_variant	Intron 14 of 18		NP_848654.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.2867+716T>C		intron_variant	Intron 23 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.1532+716T>C		intron_variant	Intron 14 of 18	1		ENSP00000258738.6
ABCB5	ENST00000441315.1	n.368+716T>C		intron_variant	Intron 3 of 7	2		ENSP00000398692.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54856 AN: 151934 Hom.: 10525 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.361 AC: 54933 AN: 152052 Hom.: 10553 Cov.: 32 AF XY: 0.365 AC XY: 27148 AN XY: 74330

African (AFR) AF: 0.407 AC: 16854 AN: 41450

American (AMR) AF: 0.452 AC: 6909 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3483 AN: 5174

South Asian (SAS) AF: 0.306 AC: 1479 AN: 4828

European-Finnish (FIN) AF: 0.368 AC: 3888 AN: 10566

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20294 AN: 67976

Other (OTH) AF: 0.362 AC: 761 AN: 2104

Alfa AF: 0.335 Hom.: 1194

Bravo AF: 0.378

Asia WGS AF: 0.476 AC: 1652 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.79
PhyloP100		-0.13
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: rs4719626; hg19: chr7-20768794;