rs6440561

Variant names:

• chr3-148640795-G-A
• rs6440561

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 0.815 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.838 AC: 34681 AN: 41392

American (AMR) AF: 0.839 AC: 12781 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2501 AN: 3468

East Asian (EAS) AF: 0.916 AC: 4699 AN: 5132

South Asian (SAS) AF: 0.897 AC: 4293 AN: 4786

European-Finnish (FIN) AF: 0.845 AC: 8927 AN: 10562

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53184 AN: 67910

Other (OTH) AF: 0.791 AC: 1671 AN: 2112

Alfa AF: 0.790 Hom.: 61619

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
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6440561; hg19: chr3-148358582;