rs7607316

Variant names:

• chr2-236613199-C-A
• rs7607316

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;