7-20690308-T-C

Variant names:

• chr7-20690308-T-C
• rs12700229
• NM_001163941.2:c.2010+4472T>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.2010+4472T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,102 control chromosomes in the GnomAD database, including 30,319 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 0.62 (30319 hom., cov: 33)
• Consequence: ABCB5 NM_001163941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.719 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	NM_001163941.2	MANE Select	c.2010+4472T>C		intron	N/A	NP_001157413.1	Q2M3G0-4
	ABCB5	NM_178559.6		c.675+4472T>C		intron	N/A	NP_848654.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB5	ENST00000404938.7	TSL:1 MANE Select	c.2010+4472T>C		intron	N/A	ENSP00000384881.2	Q2M3G0-4
	ABCB5	ENST00000258738.10	TSL:1	c.675+4472T>C		intron	N/A	ENSP00000258738.6	Q2M3G0-1

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94939 AN: 151986 Hom.: 30312 Cov.: 33

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.624 AC: 94974 AN: 152102 Hom.: 30319 Cov.: 33 AF XY: 0.620 AC XY: 46107 AN XY: 74348

African (AFR) AF: 0.536 AC: 22225 AN: 41474

American (AMR) AF: 0.562 AC: 8593 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2412 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1653 AN: 5174

South Asian (SAS) AF: 0.739 AC: 3565 AN: 4824

European-Finnish (FIN) AF: 0.653 AC: 6900 AN: 10572

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47589 AN: 67990

Other (OTH) AF: 0.638 AC: 1349 AN: 2116

Alfa AF: 0.666 Hom.: 66681

Bravo AF: 0.606

Asia WGS AF: 0.532 AC: 1853 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.37
PhyloP100		0.58
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: rs12700229; hg19: chr7-20729931;