10-5109379-A-G

Variant names:

• chr10-5109379-A-G
• rs7070041

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 0.218 in 152,220 control chromosomes in the GnomAD database, including 3,764 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 (3764 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 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: 0.218 AC: 33116 AN: 152102 Hom.: 3759 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.218 AC: 33133 AN: 152220 Hom.: 3764 Cov.: 33 AF XY: 0.215 AC XY: 16026 AN XY: 74412

African (AFR) AF: 0.173 AC: 7181 AN: 41530

American (AMR) AF: 0.216 AC: 3306 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1230 AN: 5186

South Asian (SAS) AF: 0.205 AC: 990 AN: 4826

European-Finnish (FIN) AF: 0.225 AC: 2379 AN: 10588

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16081 AN: 68016

Other (OTH) AF: 0.274 AC: 578 AN: 2112

Alfa AF: 0.219 Hom.: 555

Bravo AF: 0.218

Asia WGS AF: 0.252 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.21
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs7070041; hg19: chr10-5151571;