15-79777420-T-G

Variant names:

• chr15-79777420-T-G
• rs166870

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• 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

African (AFR) AF: 0.0476 AC: 1977 AN: 41504

American (AMR) AF: 0.0320 AC: 490 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0494 AC: 238 AN: 4820

European-Finnish (FIN) AF: 0.0357 AC: 378 AN: 10588

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0439 AC: 2985 AN: 68006

Other (OTH) AF: 0.0397 AC: 84 AN: 2114

Alfa AF: 0.00481 Hom.: 9872

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs166870; hg19: chr15-80069762;