rs7607316

chr2-236613199-C-A

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 0.315 in 151,952 control chromosomes in the GnomAD database, including 10,075 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 0.31 (10075 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47722 AN: 151834 Hom.: 10040 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.315 AC: 47800 AN: 151952 Hom.: 10075 Cov.: 32 AF XY: 0.309 AC XY: 22932 AN XY: 74278

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.309

Alfa AF: 0.241 Hom.: 2556

Bravo AF: 0.331

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.079
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7607316; hg19: chr2-237521842;