17-37746322-G-T

Variant names:

• chr17-37746322-G-T
• rs3760511
• ENST00000827939.1:n.268-833G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827939.1(ENSG00000307699):​n.268-833G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,212 control chromosomes in the GnomAD database, including 36,504 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 0.68 (36504 hom., cov: 35)
• Consequence: ENSG00000307699 ENST00000827939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 32 publications found

Genes affected

ENSG00000307699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827939.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307699	ENST00000827939.1		n.268-833G>T		intron	N/A
	ENSG00000307699	ENST00000827940.1		n.232+909G>T		intron	N/A
	ENSG00000307699	ENST00000827941.1		n.232-833G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103797 AN: 152094 Hom.: 36487 Cov.: 35

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.682 AC: 103847 AN: 152212 Hom.: 36504 Cov.: 35 AF XY: 0.670 AC XY: 49842 AN XY: 74424

African (AFR) AF: 0.815 AC: 33884 AN: 41550

American (AMR) AF: 0.591 AC: 9041 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2626 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1997 AN: 5168

South Asian (SAS) AF: 0.528 AC: 2546 AN: 4824

European-Finnish (FIN) AF: 0.538 AC: 5684 AN: 10570

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45645 AN: 68006

Other (OTH) AF: 0.695 AC: 1470 AN: 2114

Alfa AF: 0.662 Hom.: 44066

Bravo AF: 0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3760511; hg19: chr17-36106313;