chr3-39566270-G-A

Variant names:

• chr3-39566270-G-A
• rs1708080
• ENST00000827701.1:n.390-16270C>T

Variant summary

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

The ENST00000827701.1(ENSG00000307656):​n.390-16270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,084 control chromosomes in the GnomAD database, including 43,355 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 0.74 (43355 hom., cov: 32)
• Consequence: ENSG00000307656 ENST00000827701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925
• Publications: 1 publications found

Genes affected

ENSG00000307656 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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
ENSG00000307656	ENST00000827701.1	n.390-16270C>T		intron_variant	Intron 2 of 2
ENSG00000307656	ENST00000827702.1	n.227-16270C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112921 AN: 151966 Hom.: 43346 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.743 AC: 112965 AN: 152084 Hom.: 43355 Cov.: 32 AF XY: 0.744 AC XY: 55323 AN XY: 74334

African (AFR) AF: 0.527 AC: 21814 AN: 41416

American (AMR) AF: 0.786 AC: 12012 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2896 AN: 3468

East Asian (EAS) AF: 0.846 AC: 4389 AN: 5186

South Asian (SAS) AF: 0.789 AC: 3811 AN: 4828

European-Finnish (FIN) AF: 0.870 AC: 9217 AN: 10598

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56154 AN: 68002

Other (OTH) AF: 0.782 AC: 1643 AN: 2102

Alfa AF: 0.771 Hom.: 6008

Bravo AF: 0.733

Asia WGS AF: 0.793 AC: 2747 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.37
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs1708080; hg19: chr3-39607761;