chr10-49602845-T-C

Variant names:

• chr10-49602845-T-C
• rs11101179

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 0.226 in 152,222 control chromosomes in the GnomAD database, including 4,946 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 0.23 (4946 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34362 AN: 152104 Hom.: 4947 Cov.: 33

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.226 AC: 34347 AN: 152222 Hom.: 4946 Cov.: 33 AF XY: 0.224 AC XY: 16649 AN XY: 74426

African (AFR) AF: 0.0565 AC: 2348 AN: 41568

American (AMR) AF: 0.229 AC: 3493 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1079 AN: 5182

South Asian (SAS) AF: 0.149 AC: 718 AN: 4828

European-Finnish (FIN) AF: 0.312 AC: 3298 AN: 10586

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21456 AN: 67986

Other (OTH) AF: 0.251 AC: 529 AN: 2108

Alfa AF: 0.284 Hom.: 8668

Bravo AF: 0.213

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.80
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs11101179; hg19: chr10-50810891;