10-15481068-T-G

Variant names:

• chr10-15481068-T-G
• rs17369334

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 0.0551 in 152,284 control chromosomes in the GnomAD database, including 265 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 0.055 (265 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0684 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: 0.0551 AC: 8380 AN: 152164 Hom.: 266 Cov.: 33

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0551 AC: 8390 AN: 152284 Hom.: 265 Cov.: 33 AF XY: 0.0546 AC XY: 4068 AN XY: 74458

African (AFR) AF: 0.0705 AC: 2929 AN: 41556

American (AMR) AF: 0.0372 AC: 569 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0426 AC: 148 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4822

European-Finnish (FIN) AF: 0.0685 AC: 727 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0548 AC: 3730 AN: 68022

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0561 Hom.: 39

Bravo AF: 0.0536

Asia WGS AF: 0.0150 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.22
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs17369334; hg19: chr10-15523067;