rs578935

Variant names:

• chr2-136453421-T-C
• rs578935

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;