rs10488506

Variant names:

• chr7-91691671-C-T
• rs10488506

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 0.0575 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0136 AC: 565 AN: 41560

American (AMR) AF: 0.0609 AC: 931 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0585 AC: 282 AN: 4822

European-Finnish (FIN) AF: 0.0651 AC: 690 AN: 10600

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0834 AC: 5672 AN: 67996

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0757 Hom.: 256

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10488506; hg19: chr7-91320986;