chr10-44507484-G-A

Variant names:

• chr10-44507484-G-A
• rs1147967

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 0.0999 in 152,192 control chromosomes in the GnomAD database, including 994 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 0.10 (994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.0999 AC: 15198 AN: 152074 Hom.: 992 Cov.: 32

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0224

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0999 AC: 15197 AN: 152192 Hom.: 994 Cov.: 32 AF XY: 0.0983 AC XY: 7314 AN XY: 74394

African (AFR) AF: 0.0278 AC: 1153 AN: 41546

American (AMR) AF: 0.0626 AC: 958 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3472

East Asian (EAS) AF: 0.0222 AC: 115 AN: 5174

South Asian (SAS) AF: 0.154 AC: 743 AN: 4812

European-Finnish (FIN) AF: 0.139 AC: 1475 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9777 AN: 67992

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0709 Hom.: 105

Bravo AF: 0.0890

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.45
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1147967; hg19: chr10-45002932;