chr15-79806338-T-G

Variant names:

• chr15-79806338-T-G
• rs10519255

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 0.028 in 152,314 control chromosomes in the GnomAD database, including 385 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 0.028 (385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 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: 0.0281 AC: 4270 AN: 152196 Hom.: 386 Cov.: 32

Gnomad AFR AF: 0.00873

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00519

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0280 AC: 4260 AN: 152314 Hom.: 385 Cov.: 32 AF XY: 0.0332 AC XY: 2472 AN XY: 74476

African (AFR) AF: 0.00868 AC: 361 AN: 41584

American (AMR) AF: 0.0565 AC: 865 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3472

East Asian (EAS) AF: 0.335 AC: 1733 AN: 5178

South Asian (SAS) AF: 0.0406 AC: 196 AN: 4828

European-Finnish (FIN) AF: 0.0625 AC: 663 AN: 10602

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00517 AC: 352 AN: 68032

Other (OTH) AF: 0.0251 AC: 53 AN: 2114

Alfa AF: 0.00570 Hom.: 1

Bravo AF: 0.0300

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.45
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10519255; hg19: chr15-80098680;