rs1147967

Positions:

• chr10-44507484-G-A
• chr10-44507484-G-T

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 0.0999 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.0222

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.0928

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1147967; hg19: chr10-45002932;