rs1581492

chr7-99589203-G-Achr7-99589203-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 0.126 in 150,500 control chromosomes in the GnomAD database, including 1,553 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 (1553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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: 0.126 AC: 18940 AN: 150376 Hom.: 1544 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.00394

Gnomad SAS AF: 0.0682

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0646

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.126 AC: 18978 AN: 150500 Hom.: 1553 Cov.: 31 AF XY: 0.128 AC XY: 9435 AN XY: 73482

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.0985

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.00395

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0741 Hom.: 166

Bravo AF: 0.125

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.1
Dann	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1581492; hg19: chr7-99186826;