rs6440561

chr3-148640795-G-A

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 0.815 in 151,790 control chromosomes in the GnomAD database, including 50,586 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 0.81 (50586 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123570 AN: 151672 Hom.: 50537 Cov.: 28

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.815 AC: 123677 AN: 151790 Hom.: 50586 Cov.: 28 AF XY: 0.818 AC XY: 60706 AN XY: 74176

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.791

Alfa AF: 0.786 Hom.: 44637

Bravo AF: 0.815

Asia WGS AF: 0.919 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.9
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6440561; hg19: chr3-148358582;