chr10-44607048-G-A

Variant names:

• chr10-44607048-G-A
• rs6593430

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 0.876 in 152,104 control chromosomes in the GnomAD database, including 59,076 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 0.88 (59076 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71
• Publications: 3 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 = 0.938 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: 0.876 AC: 133180 AN: 151986 Hom.: 59049 Cov.: 30

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.876 AC: 133261 AN: 152104 Hom.: 59076 Cov.: 30 AF XY: 0.878 AC XY: 65279 AN XY: 74362

African (AFR) AF: 0.736 AC: 30502 AN: 41416

American (AMR) AF: 0.935 AC: 14304 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3111 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3887 AN: 5148

South Asian (SAS) AF: 0.825 AC: 3975 AN: 4818

European-Finnish (FIN) AF: 0.963 AC: 10235 AN: 10626

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64243 AN: 68014

Other (OTH) AF: 0.896 AC: 1896 AN: 2116

Alfa AF: 0.913 Hom.: 49154

Bravo AF: 0.872

Asia WGS AF: 0.794 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.35
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs6593430; hg19: chr10-45102496;