rs4241185

Positions:

• chr2-194662714-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 0.0271 in 152,142 control chromosomes in the GnomAD database, including 157 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 0.027 (157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.096 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: 0.0271 AC: 4117 AN: 152024 Hom.: 155 Cov.: 32

Gnomad AFR AF: 0.00661

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0424

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0271 AC: 4129 AN: 152142 Hom.: 157 Cov.: 32 AF XY: 0.0296 AC XY: 2198 AN XY: 74380

Gnomad4 AFR AF: 0.00659

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.00597

Gnomad4 SAS AF: 0.0549

Gnomad4 FIN AF: 0.0424

Gnomad4 NFE AF: 0.0212

Gnomad4 OTH AF: 0.0256

Alfa AF: 0.0280 Hom.: 17

Bravo AF: 0.0305

Asia WGS AF: 0.0370 AC: 128 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4241185; hg19: chr2-195527438;