chr10-121078345-T-C

Variant names:

• chr10-121078345-T-C
• rs732640

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 0.39 in 152,072 control chromosomes in the GnomAD database, including 13,574 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 0.39 (13574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59144 AN: 151952 Hom.: 13523 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.390 AC: 59257 AN: 152072 Hom.: 13574 Cov.: 32 AF XY: 0.398 AC XY: 29581 AN XY: 74362

African (AFR) AF: 0.606 AC: 25121 AN: 41466

American (AMR) AF: 0.446 AC: 6813 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3472

East Asian (EAS) AF: 0.574 AC: 2968 AN: 5174

South Asian (SAS) AF: 0.434 AC: 2093 AN: 4822

European-Finnish (FIN) AF: 0.334 AC: 3530 AN: 10570

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16755 AN: 67976

Other (OTH) AF: 0.363 AC: 769 AN: 2116

Alfa AF: 0.281 Hom.: 2959

Bravo AF: 0.407

Asia WGS AF: 0.559 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.42
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs732640; hg19: chr10-122837858;