rs11007349

Variant names:

• chr10-28998449-C-T
• rs11007349

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 0.0942 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.0941 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

African (AFR) AF: 0.0913 AC: 3789 AN: 41518

American (AMR) AF: 0.0975 AC: 1489 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2068 AN: 5160

South Asian (SAS) AF: 0.190 AC: 917 AN: 4814

European-Finnish (FIN) AF: 0.0696 AC: 737 AN: 10586

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4624 AN: 67982

Other (OTH) AF: 0.0985 AC: 208 AN: 2112

Alfa AF: 0.0816 Hom.: 83

Bravo AF: 0.0959

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.28

Splicing

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

Other links and lift over

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