chr2-35657673-T-C

Position:

• chr2-35657673-T-C

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 0.469 in 151,942 control chromosomes in the GnomAD database, including 18,299 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 0.47 (18299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71266 AN: 151824 Hom.: 18268 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.469 AC: 71331 AN: 151942 Hom.: 18299 Cov.: 32 AF XY: 0.466 AC XY: 34562 AN XY: 74246

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.442

Alfa AF: 0.276 Hom.: 628

Bravo AF: 0.480

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1401224; hg19: chr2-35882739;