rs4541776

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.628

Alfa AF: 0.628 Hom.: 8134

Bravo AF: 0.615

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4541776; hg19: chr6-121902869;