ENST00000665274.1:n.116-59261G>A

Variant names:

• chr3-161675181-G-A
• rs2404571
• ENST00000665274.1:n.116-59261G>A

Variant summary

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

The ENST00000665274.1(ENSG00000288087):​n.116-59261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,252 control chromosomes in the GnomAD database, including 62,231 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 0.90 (62231 hom., cov: 32)
• Consequence: ENSG00000288087 ENST00000665274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251
• Publications: 3 publications found

Genes affected

ENSG00000288087 (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 = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665274.1. 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
	ENSG00000288087	ENST00000665274.1		n.116-59261G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137342 AN: 152132 Hom.: 62163 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.903 AC: 137471 AN: 152252 Hom.: 62231 Cov.: 32 AF XY: 0.908 AC XY: 67581 AN XY: 74424

African (AFR) AF: 0.956 AC: 39714 AN: 41546

American (AMR) AF: 0.897 AC: 13711 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2938 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5178

South Asian (SAS) AF: 0.970 AC: 4678 AN: 4822

European-Finnish (FIN) AF: 0.910 AC: 9650 AN: 10604

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58745 AN: 68024

Other (OTH) AF: 0.870 AC: 1841 AN: 2116

Alfa AF: 0.884 Hom.: 7438

Bravo AF: 0.902

Asia WGS AF: 0.981 AC: 3412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.14
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2404571; hg19: chr3-161392969;