chr15-66967561-T-C

Variant names:

• chr15-66967561-T-C
• rs7169032

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 0.0807 in 152,244 control chromosomes in the GnomAD database, including 687 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 0.081 (687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 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: 0.0808 AC: 12296 AN: 152126 Hom.: 687 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0758

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.0807 AC: 12287 AN: 152244 Hom.: 687 Cov.: 32 AF XY: 0.0794 AC XY: 5912 AN XY: 74446

African (AFR) AF: 0.0203 AC: 844 AN: 41564

American (AMR) AF: 0.0756 AC: 1156 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.110 AC: 530 AN: 4818

European-Finnish (FIN) AF: 0.0833 AC: 884 AN: 10608

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8059 AN: 67994

Other (OTH) AF: 0.0949 AC: 200 AN: 2108

Alfa AF: 0.0846 Hom.: 144

Bravo AF: 0.0779

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.79
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs7169032; hg19: chr15-67259899;