rs196646

chr7-36317052-C-T

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 0.268 in 152,046 control chromosomes in the GnomAD database, including 5,952 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 0.27 (5952 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940

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 = 0.337 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: 0.268 AC: 40748 AN: 151928 Hom.: 5956 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.268 AC: 40765 AN: 152046 Hom.: 5952 Cov.: 32 AF XY: 0.276 AC XY: 20535 AN XY: 74290

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.250

Alfa AF: 0.287 Hom.: 8734

Bravo AF: 0.251

Asia WGS AF: 0.227 AC: 789 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	2.7
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs196646; hg19: chr7-36356661;