rs10501877

Variant names:

• chr11-98098423-T-C
• rs10501877

Your query was ambiguous. Multiple possible variants found:

• chr11-98098423-T-C
• chr11-98098423-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 0.225 in 152,018 control chromosomes in the GnomAD database, including 4,041 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 0.22 (4041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.339 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: 0.224 AC: 34099 AN: 151898 Hom.: 4036 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.225 AC: 34137 AN: 152018 Hom.: 4041 Cov.: 32 AF XY: 0.229 AC XY: 17045 AN XY: 74290

African (AFR) AF: 0.173 AC: 7159 AN: 41500

American (AMR) AF: 0.168 AC: 2570 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1796 AN: 5148

South Asian (SAS) AF: 0.352 AC: 1699 AN: 4820

European-Finnish (FIN) AF: 0.320 AC: 3371 AN: 10542

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16133 AN: 67944

Other (OTH) AF: 0.219 AC: 463 AN: 2114

Alfa AF: 0.239 Hom.: 2783

Bravo AF: 0.206

Asia WGS AF: 0.337 AC: 1168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.6
DANN	Benign	0.65
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10501877; hg19: chr11-97969151; COSMIC: COSV107158985;