chr4-141446250-C-A

Variant names:

• chr4-141446250-C-A
• rs6838494

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 0.273 in 151,920 control chromosomes in the GnomAD database, including 7,043 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 0.27 (7043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41423 AN: 151800 Hom.: 7012 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.273 AC: 41518 AN: 151920 Hom.: 7043 Cov.: 32 AF XY: 0.270 AC XY: 20064 AN XY: 74252

African (AFR) AF: 0.478 AC: 19789 AN: 41438

American (AMR) AF: 0.299 AC: 4559 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1128 AN: 5144

South Asian (SAS) AF: 0.187 AC: 901 AN: 4812

European-Finnish (FIN) AF: 0.128 AC: 1348 AN: 10568

Middle Eastern (MID) AF: 0.283 AC: 82 AN: 290

European-Non Finnish (NFE) AF: 0.183 AC: 12415 AN: 67920

Other (OTH) AF: 0.268 AC: 564 AN: 2106

Alfa AF: 0.183 Hom.: 676

Bravo AF: 0.294

Asia WGS AF: 0.226 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.2
DANN	Benign	0.71
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs6838494; hg19: chr4-142367404;