chr7-37523875-G-T

Variant names:

• chr7-37523875-G-T
• rs718015
• ENST00000731302.1:n.459-6698G>T

Variant summary

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

The ENST00000731302.1(ENSG00000295610):​n.459-6698G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,866 control chromosomes in the GnomAD database, including 19,238 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 0.50 (19238 hom., cov: 31)
• Consequence: ENSG00000295610 ENST00000731302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 5 publications found

Genes affected

ENSG00000295610 (HGNC:):

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 = 0.533 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731302.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295610	ENST00000731302.1		n.459-6698G>T		intron	N/A
	ENSG00000295610	ENST00000731303.1		n.459-22971G>T		intron	N/A
	ENSG00000295610	ENST00000731304.1		n.63-6698G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75946 AN: 151748 Hom.: 19235 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.500 AC: 75989 AN: 151866 Hom.: 19238 Cov.: 31 AF XY: 0.502 AC XY: 37262 AN XY: 74216

African (AFR) AF: 0.422 AC: 17468 AN: 41382

American (AMR) AF: 0.488 AC: 7436 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2048 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2620 AN: 5170

South Asian (SAS) AF: 0.480 AC: 2311 AN: 4810

European-Finnish (FIN) AF: 0.567 AC: 5978 AN: 10542

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36521 AN: 67940

Other (OTH) AF: 0.524 AC: 1105 AN: 2108

Alfa AF: 0.507 Hom.: 2509

Bravo AF: 0.493

Asia WGS AF: 0.461 AC: 1600 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	1.7
DANN	Benign	0.50
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs718015; hg19: chr7-37563478;