chr10-49544407-G-A

Variant names:

• chr10-49544407-G-A
• rs4453140

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 0.77 in 151,968 control chromosomes in the GnomAD database, including 45,382 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 0.77 (45382 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116937 AN: 151850 Hom.: 45383 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.770 AC: 116973 AN: 151968 Hom.: 45382 Cov.: 31 AF XY: 0.771 AC XY: 57256 AN XY: 74270

African (AFR) AF: 0.679 AC: 28104 AN: 41404

American (AMR) AF: 0.728 AC: 11124 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2719 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4111 AN: 5162

South Asian (SAS) AF: 0.752 AC: 3621 AN: 4814

European-Finnish (FIN) AF: 0.860 AC: 9083 AN: 10556

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55578 AN: 67972

Other (OTH) AF: 0.793 AC: 1676 AN: 2114

Alfa AF: 0.769 Hom.: 5459

Bravo AF: 0.754

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.082
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs4453140; hg19: chr10-50752453;