17-39754115-C-T

Variant names:

• chr17-39754115-C-T
• rs2941522

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 0.495 in 152,090 control chromosomes in the GnomAD database, including 18,902 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 0.49 (18902 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 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: 0.495 AC: 75211 AN: 151982 Hom.: 18907 Cov.: 34

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.495 AC: 75220 AN: 152090 Hom.: 18902 Cov.: 34 AF XY: 0.495 AC XY: 36812 AN XY: 74362

African (AFR) AF: 0.439 AC: 18223 AN: 41516

American (AMR) AF: 0.567 AC: 8672 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1859 AN: 3468

East Asian (EAS) AF: 0.705 AC: 3631 AN: 5152

South Asian (SAS) AF: 0.601 AC: 2902 AN: 4830

European-Finnish (FIN) AF: 0.415 AC: 4396 AN: 10596

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.500 AC: 33950 AN: 67928

Other (OTH) AF: 0.531 AC: 1121 AN: 2112

Alfa AF: 0.468 Hom.: 2772

Bravo AF: 0.508

Asia WGS AF: 0.574 AC: 1987 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.2
DANN	Benign	0.79
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2941522; hg19: chr17-37910368;