rs196646

Variant names:

• chr7-36317052-C-T
• rs196646

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 0.268 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.181 AC: 7521 AN: 41468

American (AMR) AF: 0.303 AC: 4621 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1035 AN: 3472

East Asian (EAS) AF: 0.122 AC: 633 AN: 5184

South Asian (SAS) AF: 0.351 AC: 1690 AN: 4814

European-Finnish (FIN) AF: 0.411 AC: 4327 AN: 10522

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 19973 AN: 67998

Other (OTH) AF: 0.250 AC: 527 AN: 2112

Alfa AF: 0.283 Hom.: 10641

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
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs196646; hg19: chr7-36356661;