rs35593994

Positions:

• chr2-203706103-G-A
• chr2-203706103-G-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 0.345 in 150,864 control chromosomes in the GnomAD database, including 9,169 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 0.35 (9169 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 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: 0.345 AC: 52071 AN: 150746 Hom.: 9170 Cov.: 28

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.345 AC: 52077 AN: 150864 Hom.: 9169 Cov.: 28 AF XY: 0.346 AC XY: 25488 AN XY: 73658

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.336

Alfa AF: 0.339 Hom.: 1099

Bravo AF: 0.338

Asia WGS AF: 0.451 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35593994; hg19: chr2-204570826;