rs1725021

Variant names:

• chr7-137208573-T-C
• rs1725021

Variant summary

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

The variant allele was found at a frequency of 0.438 in 151,848 control chromosomes in the GnomAD database, including 14,878 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 0.44 (14878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 4 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66381 AN: 151730 Hom.: 14858 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.438 AC: 66443 AN: 151848 Hom.: 14878 Cov.: 31 AF XY: 0.443 AC XY: 32867 AN XY: 74170

African (AFR) AF: 0.518 AC: 21460 AN: 41432

American (AMR) AF: 0.398 AC: 6061 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3467 AN: 5124

South Asian (SAS) AF: 0.504 AC: 2421 AN: 4808

European-Finnish (FIN) AF: 0.455 AC: 4803 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25784 AN: 67920

Other (OTH) AF: 0.406 AC: 856 AN: 2110

Alfa AF: 0.398 Hom.: 7007

Bravo AF: 0.435

Asia WGS AF: 0.581 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs1725021; hg19: chr7-136893320;