rs578935

Positions:

• chr2-136453421-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 0.127 in 152,210 control chromosomes in the GnomAD database, including 1,403 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 0.13 (1403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 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: 0.127 AC: 19306 AN: 152092 Hom.: 1398 Cov.: 32

Gnomad AFR AF: 0.0932

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.127 AC: 19332 AN: 152210 Hom.: 1403 Cov.: 32 AF XY: 0.130 AC XY: 9635 AN XY: 74396

Gnomad4 AFR AF: 0.0935

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.174

Alfa AF: 0.136 Hom.: 3362

Bravo AF: 0.124

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs578935; hg19: chr2-137210991;