rs2968864

Positions:

• chr7-150925074-T-C

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 0.164 in 152,180 control chromosomes in the GnomAD database, including 2,723 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 0.16 (2723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 25009 AN: 152062 Hom.: 2719 Cov.: 32

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.164 AC: 25005 AN: 152180 Hom.: 2723 Cov.: 32 AF XY: 0.161 AC XY: 11959 AN XY: 74390

Gnomad4 AFR AF: 0.0418

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0478

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.183

Alfa AF: 0.226 Hom.: 5478

Bravo AF: 0.157

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2968864; hg19: chr7-150622162;