7-131921403-G-A

Variant names:

• chr7-131921403-G-A
• rs10271989
• ENST00000415393.1:n.353-4836G>A

Variant summary

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

The ENST00000415393.1(ENSG00000224865):​n.353-4836G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,838 control chromosomes in the GnomAD database, including 30,917 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 0.60 (30917 hom., cov: 30)
• Consequence: ENSG00000224865 ENST00000415393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44
• Publications: 5 publications found

Genes affected

ENSG00000224865 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928782	NR_110836.1	n.353-4836G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224865	ENST00000415393.1	n.353-4836G>A		intron_variant	Intron 1 of 5	2
ENSG00000224865	ENST00000452219.5	n.86-10720G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91680 AN: 151722 Hom.: 30916 Cov.: 30

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.604 AC: 91697 AN: 151838 Hom.: 30917 Cov.: 30 AF XY: 0.612 AC XY: 45370 AN XY: 74188

African (AFR) AF: 0.282 AC: 11660 AN: 41378

American (AMR) AF: 0.746 AC: 11389 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2201 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4973 AN: 5156

South Asian (SAS) AF: 0.682 AC: 3270 AN: 4792

European-Finnish (FIN) AF: 0.714 AC: 7522 AN: 10536

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48530 AN: 67926

Other (OTH) AF: 0.647 AC: 1364 AN: 2108

Alfa AF: 0.681 Hom.: 23353

Bravo AF: 0.593

Asia WGS AF: 0.760 AC: 2638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	18
DANN	Benign	0.55
PhyloP100		2.4
Mutation Taster		=46/54	disease causing

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10271989; hg19: chr7-131606162;