rs4541776

Variant names:

• chr6-121581723-G-A
• rs4541776

Your query was ambiguous. Multiple possible variants found:

• chr6-121581723-G-A
• chr6-121581723-G-T

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 0.618 in 151,978 control chromosomes in the GnomAD database, including 29,191 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 0.62 (29191 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.618 AC: 93915 AN: 151862 Hom.: 29187 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.618 AC: 93970 AN: 151978 Hom.: 29191 Cov.: 32 AF XY: 0.613 AC XY: 45525 AN XY: 74284

African (AFR) AF: 0.628 AC: 26050 AN: 41454

American (AMR) AF: 0.509 AC: 7762 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2263 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3492 AN: 5156

South Asian (SAS) AF: 0.518 AC: 2500 AN: 4824

European-Finnish (FIN) AF: 0.628 AC: 6613 AN: 10530

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43318 AN: 67970

Other (OTH) AF: 0.628 AC: 1323 AN: 2108

Alfa AF: 0.632 Hom.: 20118

Bravo AF: 0.615

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs4541776; hg19: chr6-121902869;