rs4241185

Variant names:

• chr2-194662714-T-C
• rs4241185

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.00659 AC: 274 AN: 41568

American (AMR) AF: 0.100 AC: 1531 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3468

East Asian (EAS) AF: 0.00597 AC: 31 AN: 5190

South Asian (SAS) AF: 0.0549 AC: 265 AN: 4824

European-Finnish (FIN) AF: 0.0424 AC: 449 AN: 10598

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.0212 AC: 1441 AN: 67900

Other (OTH) AF: 0.0256 AC: 54 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4241185; hg19: chr2-195527438;