chr2-203705655-G-A

Position:

• chr2-203705655-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 0.345 in 151,938 control chromosomes in the GnomAD database, including 9,204 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 0.34 (9204 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 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: 0.345 AC: 52383 AN: 151820 Hom.: 9205 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.345 AC: 52389 AN: 151938 Hom.: 9204 Cov.: 31 AF XY: 0.346 AC XY: 25685 AN XY: 74250

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.338

Alfa AF: 0.348 Hom.: 1481

Bravo AF: 0.338

Asia WGS AF: 0.449 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.23
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181098; hg19: chr2-204570378;