3-107514250-T-G

Variant names:

• chr3-107514250-T-G
• rs10511260

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 0.219 in 151,950 control chromosomes in the GnomAD database, including 4,418 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 (4418 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 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: 0.219 AC: 33267 AN: 151832 Hom.: 4420 Cov.: 31

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.219 AC: 33263 AN: 151950 Hom.: 4418 Cov.: 31 AF XY: 0.218 AC XY: 16187 AN XY: 74276

African (AFR) AF: 0.0668 AC: 2770 AN: 41456

American (AMR) AF: 0.220 AC: 3360 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3472

East Asian (EAS) AF: 0.131 AC: 677 AN: 5178

South Asian (SAS) AF: 0.256 AC: 1225 AN: 4792

European-Finnish (FIN) AF: 0.282 AC: 2973 AN: 10526

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.298 AC: 20226 AN: 67942

Other (OTH) AF: 0.242 AC: 509 AN: 2106

Alfa AF: 0.273 Hom.: 19082

Bravo AF: 0.208

Asia WGS AF: 0.173 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.53
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10511260; hg19: chr3-107233097;