chr4-41282694-T-C

Variant names:

• chr4-41282694-T-C
• rs4861096

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 0.189 in 152,104 control chromosomes in the GnomAD database, including 3,272 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 0.19 (3272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28621 AN: 151984 Hom.: 3257 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.189 AC: 28677 AN: 152104 Hom.: 3272 Cov.: 32 AF XY: 0.192 AC XY: 14262 AN XY: 74368

African (AFR) AF: 0.122 AC: 5059 AN: 41512

American (AMR) AF: 0.260 AC: 3968 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.536 AC: 2763 AN: 5158

South Asian (SAS) AF: 0.333 AC: 1605 AN: 4816

European-Finnish (FIN) AF: 0.146 AC: 1549 AN: 10576

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12439 AN: 67974

Other (OTH) AF: 0.176 AC: 371 AN: 2110

Alfa AF: 0.182 Hom.: 5203

Bravo AF: 0.195

Asia WGS AF: 0.400 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4861096; hg19: chr4-41284711;