rs10499903

Positions:

• chr7-91230302-A-G
• chr7-91230302-A-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 0.162 in 152,176 control chromosomes in the GnomAD database, including 2,275 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 0.16 (2275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.162 AC: 24569 AN: 152058 Hom.: 2264 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.162 AC: 24610 AN: 152176 Hom.: 2275 Cov.: 32 AF XY: 0.168 AC XY: 12470 AN XY: 74390

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.161

Alfa AF: 0.102 Hom.: 199

Bravo AF: 0.159

Asia WGS AF: 0.272 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499903; hg19: chr7-90859617;