15-94622351-T-G

Variant names:

• chr15-94622351-T-G
• rs1014922

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 0.153 in 152,152 control chromosomes in the GnomAD database, including 2,417 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 0.15 (2417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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: 0.153 AC: 23231 AN: 152036 Hom.: 2408 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.153 AC: 23278 AN: 152152 Hom.: 2417 Cov.: 32 AF XY: 0.151 AC XY: 11236 AN XY: 74422

African (AFR) AF: 0.293 AC: 12143 AN: 41496

American (AMR) AF: 0.121 AC: 1842 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3472

East Asian (EAS) AF: 0.275 AC: 1414 AN: 5150

South Asian (SAS) AF: 0.0945 AC: 456 AN: 4824

European-Finnish (FIN) AF: 0.0817 AC: 867 AN: 10610

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0846 AC: 5754 AN: 68000

Other (OTH) AF: 0.163 AC: 344 AN: 2116

Alfa AF: 0.122 Hom.: 2743

Bravo AF: 0.165

Asia WGS AF: 0.224 AC: 777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.5
DANN	Benign	0.87
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1014922; hg19: chr15-95165580;