chr7-45937683-G-A

Variant names:

• chr7-45937683-G-A
• rs2960436

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 0.494 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
• Publications: 16 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.600 AC: 24901 AN: 41472

American (AMR) AF: 0.376 AC: 5743 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1793 AN: 3472

East Asian (EAS) AF: 0.752 AC: 3853 AN: 5126

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4822

European-Finnish (FIN) AF: 0.381 AC: 4021 AN: 10566

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30943 AN: 67942

Other (OTH) AF: 0.482 AC: 1018 AN: 2110

Alfa AF: 0.479 Hom.: 28046

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2960436; hg19: chr7-45977282;