chr2-35683934-G-A

Position:

• chr2-35683934-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 0.405 in 152,004 control chromosomes in the GnomAD database, including 14,587 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 0.41 (14587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 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: 0.406 AC: 61600 AN: 151884 Hom.: 14583 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.405 AC: 61620 AN: 152004 Hom.: 14587 Cov.: 32 AF XY: 0.398 AC XY: 29543 AN XY: 74256

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.446

Alfa AF: 0.519 Hom.: 26929

Bravo AF: 0.398

Asia WGS AF: 0.215 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
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: rs925910; hg19: chr2-35909000;