chr6-102831899-G-C

Variant names:

• chr6-102831899-G-C
• rs10499035

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 0.0223 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.00499 AC: 207 AN: 41514

American (AMR) AF: 0.0577 AC: 878 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3466

East Asian (EAS) AF: 0.0660 AC: 339 AN: 5134

South Asian (SAS) AF: 0.0579 AC: 279 AN: 4822

European-Finnish (FIN) AF: 0.0268 AC: 284 AN: 10604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1292 AN: 67916

Other (OTH) AF: 0.0237 AC: 50 AN: 2114

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10499035; hg19: chr6-103279774;