rs7606972

Variant names:

• chr2-136699130-G-T
• rs7606972

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.658 in 152,096 control chromosomes in the GnomAD database, including 33,295 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 0.66 (33295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Benign. Variant got -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 = 0.74 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: 0.659 AC: 100107 AN: 151978 Hom.: 33295 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.658 AC: 100148 AN: 152096 Hom.: 33295 Cov.: 32 AF XY: 0.663 AC XY: 49305 AN XY: 74350

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.667

Alfa AF: 0.669 Hom.: 5360

Bravo AF: 0.662

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7606972; hg19: chr2-137456700;