rs2960436

Positions:

• chr7-45937683-G-A

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 0.494 in 152,004 control chromosomes in the GnomAD database, including 19,241 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 0.49 (19241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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: 0.494 AC: 75082 AN: 151886 Hom.: 19240 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.494 AC: 75113 AN: 152004 Hom.: 19241 Cov.: 32 AF XY: 0.489 AC XY: 36316 AN XY: 74270

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.482

Alfa AF: 0.472 Hom.: 3199

Bravo AF: 0.501

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2960436; hg19: chr7-45977282;