rs510319

chr7-126163907-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 0.347 in 151,652 control chromosomes in the GnomAD database, including 12,832 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 0.35 (12832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 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: 0.347 AC: 52513 AN: 151534 Hom.: 12785 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.347 AC: 52603 AN: 151652 Hom.: 12832 Cov.: 32 AF XY: 0.348 AC XY: 25792 AN XY: 74164

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.281

Alfa AF: 0.197 Hom.: 5975

Bravo AF: 0.356

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.98
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: rs510319; hg19: chr7-125803961;