chr17-39625357-G-C

Position:

• chr17-39625357-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.763 in 152,002 control chromosomes in the GnomAD database, including 44,800 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 0.76 (44800 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115895 AN: 151884 Hom.: 44747 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.763 AC: 116015 AN: 152002 Hom.: 44800 Cov.: 31 AF XY: 0.759 AC XY: 56349 AN XY: 74282

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.781

Alfa AF: 0.742 Hom.: 2298

Bravo AF: 0.751

Asia WGS AF: 0.686 AC: 2387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4795390; hg19: chr17-37781610;