rs10488506

chr7-91691671-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 0.0575 in 152,224 control chromosomes in the GnomAD database, including 341 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 0.057 (341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0816 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: 0.0575 AC: 8751 AN: 152106 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0575 AC: 8748 AN: 152224 Hom.: 341 Cov.: 32 AF XY: 0.0573 AC XY: 4267 AN XY: 74428

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0609

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0585

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0834

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0755 Hom.: 225

Bravo AF: 0.0560

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.86
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488506; hg19: chr7-91320986;