rs11004422

Variant names:

• chr10-46097486-T-C
• rs11004422

Your query was ambiguous. Multiple possible variants found:

• chr10-46097486-T-C
• chr10-46097486-T-G

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 0.467 in 151,744 control chromosomes in the GnomAD database, including 16,796 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 0.47 (16796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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: 0.467 AC: 70827 AN: 151626 Hom.: 16765 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.467 AC: 70906 AN: 151744 Hom.: 16796 Cov.: 32 AF XY: 0.468 AC XY: 34712 AN XY: 74116

African (AFR) AF: 0.439 AC: 18161 AN: 41348

American (AMR) AF: 0.452 AC: 6888 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2427 AN: 5142

South Asian (SAS) AF: 0.616 AC: 2965 AN: 4814

European-Finnish (FIN) AF: 0.404 AC: 4264 AN: 10542

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32510 AN: 67872

Other (OTH) AF: 0.490 AC: 1029 AN: 2102

Alfa AF: 0.478 Hom.: 2348

Bravo AF: 0.463

Asia WGS AF: 0.535 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11004422; hg19: chr10-51498336;