rs1480597

chr10-44665661-C-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 0.13 in 152,202 control chromosomes in the GnomAD database, including 1,508 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 0.13 (1508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19854 AN: 152084 Hom.: 1508 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19859 AN: 152202 Hom.: 1508 Cov.: 32 AF XY: 0.126 AC XY: 9393 AN XY: 74400

Gnomad4 AFR AF: 0.0852

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.125

Alfa AF: 0.160 Hom.: 4535

Bravo AF: 0.129

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1480597; hg19: chr10-45161109;