chr3-39346789-G-A

Variant names:

• chr3-39346789-G-A
• rs2201965
• ENST00000655387.2:n.434+34115C>T

Variant summary

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

The ENST00000655387.2(ENSG00000287780):​n.434+34115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,094 control chromosomes in the GnomAD database, including 37,185 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 0.70 (37185 hom., cov: 32)
• Consequence: ENSG00000287780 ENST00000655387.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 3 publications found

Genes affected

ENSG00000287780 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655387.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287780	ENST00000655387.2		n.434+34115C>T		intron	N/A
	ENSG00000287780	ENST00000836879.1		n.287+34115C>T		intron	N/A
	ENSG00000287780	ENST00000836880.1		n.372+34115C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105822 AN: 151976 Hom.: 37161 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.696 AC: 105896 AN: 152094 Hom.: 37185 Cov.: 32 AF XY: 0.701 AC XY: 52072 AN XY: 74328

African (AFR) AF: 0.621 AC: 25748 AN: 41478

American (AMR) AF: 0.757 AC: 11580 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2378 AN: 3466

East Asian (EAS) AF: 0.754 AC: 3893 AN: 5166

South Asian (SAS) AF: 0.790 AC: 3804 AN: 4816

European-Finnish (FIN) AF: 0.737 AC: 7788 AN: 10572

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48293 AN: 67980

Other (OTH) AF: 0.717 AC: 1515 AN: 2114

Alfa AF: 0.705 Hom.: 30978

Bravo AF: 0.693

Asia WGS AF: 0.763 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2201965; hg19: chr3-39388280;