rs6841405

Variant names:

• chr4-64201688-G-A
• rs6841405

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 0.291 in 141,540 control chromosomes in the GnomAD database, including 6,672 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 0.29 (6672 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 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: 0.291 AC: 41189 AN: 141550 Hom.: 6671 Cov.: 24

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.291 AC: 41195 AN: 141540 Hom.: 6672 Cov.: 24 AF XY: 0.290 AC XY: 19838 AN XY: 68402

African (AFR) AF: 0.154 AC: 5955 AN: 38782

American (AMR) AF: 0.389 AC: 5413 AN: 13912

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 794 AN: 3308

East Asian (EAS) AF: 0.149 AC: 736 AN: 4926

South Asian (SAS) AF: 0.399 AC: 1792 AN: 4496

European-Finnish (FIN) AF: 0.264 AC: 2065 AN: 7814

Middle Eastern (MID) AF: 0.237 AC: 64 AN: 270

European-Non Finnish (NFE) AF: 0.359 AC: 23412 AN: 65200

Other (OTH) AF: 0.302 AC: 588 AN: 1944

Alfa AF: 0.340 Hom.: 898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.084
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6841405; hg19: chr4-65067406;