rs10499035

Variant names:

• chr6-102831899-G-C
• rs10499035

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 0.0223 in 151,980 control chromosomes in the GnomAD database, including 76 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 0.022 (76 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0602 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: 0.0223 AC: 3379 AN: 151862 Hom.: 72 Cov.: 32

Gnomad AFR AF: 0.00500

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0223 AC: 3392 AN: 151980 Hom.: 76 Cov.: 32 AF XY: 0.0237 AC XY: 1763 AN XY: 74272

Gnomad4 AFR AF: 0.00499

Gnomad4 AMR AF: 0.0577

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0660

Gnomad4 SAS AF: 0.0579

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0190

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0223 Hom.: 9

Bravo AF: 0.0242

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.27
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499035; hg19: chr6-103279774;