ENST00000715880.1:n.112-34743C>T

Variant names:

• chr2-57817085-G-A
• rs2717055
• ENST00000715880.1:n.112-34743C>T

Variant summary

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

The ENST00000715880.1(ENSG00000293611):​n.112-34743C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,726 control chromosomes in the GnomAD database, including 28,767 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 0.62 (28767 hom., cov: 32)
• Consequence: ENSG00000293611 ENST00000715880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 6 publications found

Genes affected

ENSG00000293611 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715880.1. 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
	ENSG00000293611	ENST00000715880.1		n.112-34743C>T		intron	N/A
	ENSG00000293611	ENST00000715881.1		n.122-34743C>T		intron	N/A
	ENSG00000285755	ENST00000811253.1		n.103-34747C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93339 AN: 151608 Hom.: 28744 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.616 AC: 93420 AN: 151726 Hom.: 28767 Cov.: 32 AF XY: 0.615 AC XY: 45590 AN XY: 74142

African (AFR) AF: 0.595 AC: 24654 AN: 41444

American (AMR) AF: 0.588 AC: 8936 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2314 AN: 3466

East Asian (EAS) AF: 0.623 AC: 3228 AN: 5180

South Asian (SAS) AF: 0.562 AC: 2709 AN: 4820

European-Finnish (FIN) AF: 0.650 AC: 6861 AN: 10558

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42545 AN: 67744

Other (OTH) AF: 0.622 AC: 1313 AN: 2110

Alfa AF: 0.603 Hom.: 4786

Bravo AF: 0.609

Asia WGS AF: 0.602 AC: 2086 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.74
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2717055; hg19: chr2-58044220;