10-120379523-C-G

Variant names:

• chr10-120379523-C-G
• rs7080041

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 0.704 in 152,066 control chromosomes in the GnomAD database, including 44,042 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 0.70 (44042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 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: 0.704 AC: 107020 AN: 151948 Hom.: 44056 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.704 AC: 107008 AN: 152066 Hom.: 44042 Cov.: 31 AF XY: 0.703 AC XY: 52244 AN XY: 74356

African (AFR) AF: 0.248 AC: 10252 AN: 41420

American (AMR) AF: 0.796 AC: 12167 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3114 AN: 3470

East Asian (EAS) AF: 0.650 AC: 3342 AN: 5140

South Asian (SAS) AF: 0.745 AC: 3589 AN: 4816

European-Finnish (FIN) AF: 0.843 AC: 8933 AN: 10600

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 62959 AN: 68018

Other (OTH) AF: 0.765 AC: 1618 AN: 2114

Alfa AF: 0.714 Hom.: 2851

Bravo AF: 0.681

Asia WGS AF: 0.632 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7080041; hg19: chr10-122139035;