10-80122614-T-C

Variant names:

• chr10-80122614-T-C
• rs3851050

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 0.346 in 152,042 control chromosomes in the GnomAD database, including 9,533 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 0.35 (9533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 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: 0.346 AC: 52636 AN: 151924 Hom.: 9539 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.346 AC: 52653 AN: 152042 Hom.: 9533 Cov.: 32 AF XY: 0.343 AC XY: 25459 AN XY: 74312

African (AFR) AF: 0.259 AC: 10736 AN: 41476

American (AMR) AF: 0.309 AC: 4715 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1399 AN: 5160

South Asian (SAS) AF: 0.330 AC: 1589 AN: 4822

European-Finnish (FIN) AF: 0.361 AC: 3812 AN: 10560

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27688 AN: 67970

Other (OTH) AF: 0.349 AC: 736 AN: 2110

Alfa AF: 0.381 Hom.: 49643

Bravo AF: 0.338

Asia WGS AF: 0.309 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.80
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs3851050; hg19: chr10-81882370;