chr15-66697177-C-T

Variant names:

• chr15-66697177-C-T
• rs11857194

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 0.233 in 152,026 control chromosomes in the GnomAD database, including 4,161 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 0.23 (4161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.233 AC: 35417 AN: 151908 Hom.: 4163 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.233 AC: 35421 AN: 152026 Hom.: 4161 Cov.: 32 AF XY: 0.230 AC XY: 17086 AN XY: 74314

African (AFR) AF: 0.227 AC: 9404 AN: 41444

American (AMR) AF: 0.203 AC: 3094 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3470

East Asian (EAS) AF: 0.148 AC: 766 AN: 5170

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4816

European-Finnish (FIN) AF: 0.210 AC: 2220 AN: 10574

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17262 AN: 67990

Other (OTH) AF: 0.236 AC: 496 AN: 2104

Alfa AF: 0.250 Hom.: 12844

Bravo AF: 0.231

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.091
DANN	Benign	0.46
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11857194; hg19: chr15-66989515;