rs10499903

Variant names:

• chr7-91230302-A-G
• rs10499903

Your query was ambiguous. Multiple possible variants found:

• chr7-91230302-A-G
• chr7-91230302-A-T

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 0.162 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.113 AC: 4685 AN: 41546

American (AMR) AF: 0.223 AC: 3410 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2028 AN: 5148

South Asian (SAS) AF: 0.172 AC: 827 AN: 4820

European-Finnish (FIN) AF: 0.210 AC: 2220 AN: 10592

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10435 AN: 67996

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.102 Hom.: 203

Bravo AF: 0.159

Asia WGS AF: 0.272 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10499903; hg19: chr7-90859617;