rs6440561

Variant names:

• chr3-148640795-G-A
• rs6440561

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;