chr7-150926049-C-T

Variant names:

• chr7-150926049-C-T
• rs2968863

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 0.166 in 152,202 control chromosomes in the GnomAD database, including 2,731 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 0.17 (2731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25225 AN: 152084 Hom.: 2726 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.166 AC: 25227 AN: 152202 Hom.: 2731 Cov.: 32 AF XY: 0.162 AC XY: 12074 AN XY: 74422

Gnomad4 AFR AF: 0.0474

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0476

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.184

Alfa AF: 0.224 Hom.: 5209

Bravo AF: 0.158

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	-0.94
CADD	Benign	2.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2968863; hg19: chr7-150623137;