17-3126260-T-C

Variant names:

• chr17-3126260-T-C
• rs12449465

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 0.142 in 152,230 control chromosomes in the GnomAD database, including 1,568 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 0.14 (1568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 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: 0.142 AC: 21620 AN: 152112 Hom.: 1571 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.142 AC: 21623 AN: 152230 Hom.: 1568 Cov.: 32 AF XY: 0.144 AC XY: 10720 AN XY: 74442

African (AFR) AF: 0.157 AC: 6512 AN: 41534

American (AMR) AF: 0.157 AC: 2402 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3470

East Asian (EAS) AF: 0.185 AC: 960 AN: 5190

South Asian (SAS) AF: 0.246 AC: 1183 AN: 4812

European-Finnish (FIN) AF: 0.117 AC: 1245 AN: 10604

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8365 AN: 67996

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.134 Hom.: 4575

Bravo AF: 0.148

Asia WGS AF: 0.217 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.83
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12449465; hg19: chr17-3029554;