rs10499889

Variant names:

• chr7-85491748-T-C
• rs10499889

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 0.348 in 151,626 control chromosomes in the GnomAD database, including 10,066 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 0.35 (10066 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

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 (NFE) allele frequency at 95% confidence interval = 0.421 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: 0.348 AC: 52795 AN: 151508 Hom.: 10069 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.348 AC: 52789 AN: 151626 Hom.: 10066 Cov.: 31 AF XY: 0.342 AC XY: 25370 AN XY: 74084

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.0327

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.365

Alfa AF: 0.393 Hom.: 8595

Bravo AF: 0.335

Asia WGS AF: 0.200 AC: 699 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
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: rs10499889; hg19: chr7-85121064;