rs6842241

Variant names:

• chr4-147479667-C-A
• rs6842241

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 0.219 in 151,934 control chromosomes in the GnomAD database, including 4,625 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 0.22 (4625 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 49 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 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: 0.219 AC: 33282 AN: 151814 Hom.: 4612 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.219 AC: 33332 AN: 151934 Hom.: 4625 Cov.: 32 AF XY: 0.218 AC XY: 16183 AN XY: 74250

African (AFR) AF: 0.397 AC: 16441 AN: 41384

American (AMR) AF: 0.153 AC: 2335 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1158 AN: 5178

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4810

European-Finnish (FIN) AF: 0.148 AC: 1566 AN: 10570

Middle Eastern (MID) AF: 0.206 AC: 59 AN: 286

European-Non Finnish (NFE) AF: 0.139 AC: 9444 AN: 67940

Other (OTH) AF: 0.200 AC: 422 AN: 2110

Alfa AF: 0.162 Hom.: 6901

Bravo AF: 0.230

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.053
DANN	Benign	0.29
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6842241; hg19: chr4-148400819;