15-79777420-T-G

Variant names:

• chr15-79777420-T-G
• rs166870

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0418 in 152,172 control chromosomes in the GnomAD database, including 170 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 0.042 (170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0418 (6363/152172) while in subpopulation SAS AF= 0.0494 (238/4820). AF 95% confidence interval is 0.0459. There are 170 homozygotes in gnomad4. There are 3142 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 170 gene

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: 0.0418 AC: 6358 AN: 152054 Hom.: 170 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0418 AC: 6363 AN: 152172 Hom.: 170 Cov.: 32 AF XY: 0.0422 AC XY: 3142 AN XY: 74378

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.0320

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0494

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0160 Hom.: 2744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166870; hg19: chr15-80069762;