NM_001163941.2:c.3025-406C>T

Variant names:

• chr7-20742471-C-T
• rs10231520
• NM_001163941.2:c.3025-406C>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.3025-406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,052 control chromosomes in the GnomAD database, including 6,901 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 0.29 (6901 hom., cov: 33)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB5	NM_001163941.2	c.3025-406C>T		intron_variant	Intron 24 of 27	ENST00000404938.7	NP_001157413.1
ABCB5	NM_178559.6	c.1690-406C>T		intron_variant	Intron 15 of 18		NP_848654.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB5	ENST00000404938.7	c.3025-406C>T		intron_variant	Intron 24 of 27	1	NM_001163941.2	ENSP00000384881.2
ABCB5	ENST00000258738.10	c.1690-406C>T		intron_variant	Intron 15 of 18	1		ENSP00000258738.6
ABCB5	ENST00000441315.1	n.526-406C>T		intron_variant	Intron 4 of 7	2		ENSP00000398692.1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44065 AN: 151934 Hom.: 6905 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.290 AC: 44059 AN: 152052 Hom.: 6901 Cov.: 33 AF XY: 0.289 AC XY: 21449 AN XY: 74320

African (AFR) AF: 0.167 AC: 6945 AN: 41486

American (AMR) AF: 0.263 AC: 4023 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1035 AN: 3466

East Asian (EAS) AF: 0.302 AC: 1561 AN: 5172

South Asian (SAS) AF: 0.313 AC: 1512 AN: 4824

European-Finnish (FIN) AF: 0.344 AC: 3624 AN: 10534

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24316 AN: 67964

Other (OTH) AF: 0.325 AC: 686 AN: 2112

Alfa AF: 0.336 Hom.: 18005

Bravo AF: 0.283

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.20
PhyloP100		-0.54
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: rs10231520; hg19: chr7-20782094;