chr10-28998449-C-T

Variant names:

• chr10-28998449-C-T
• rs11007349

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 0.0942 in 152,116 control chromosomes in the GnomAD database, including 1,061 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 0.094 (1061 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.0941 AC: 14306 AN: 151998 Hom.: 1053 Cov.: 32

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0696

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0942 AC: 14333 AN: 152116 Hom.: 1061 Cov.: 32 AF XY: 0.0971 AC XY: 7216 AN XY: 74344

Gnomad4 AFR AF: 0.0913

Gnomad4 AMR AF: 0.0975

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0696

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.0985

Alfa AF: 0.0804 Hom.: 77

Bravo AF: 0.0959

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11007349; hg19: chr10-29287378; COSMIC: COSV57174823;