ENST00000797088.1:n.295-5906T>C

Variant names:

• chr2-223404472-A-G
• rs1921649
• ENST00000797088.1:n.295-5906T>C

Variant summary

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

The ENST00000797088.1(ENSG00000303770):​n.295-5906T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,904 control chromosomes in the GnomAD database, including 31,768 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 0.64 (31768 hom., cov: 32)
• Consequence: ENSG00000303770 ENST00000797088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 1 publications found

Genes affected

ENSG00000303770 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797088.1. 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
	ENSG00000303770	ENST00000797088.1		n.295-5906T>C		intron	N/A
	ENSG00000303770	ENST00000797089.1		n.149-5906T>C		intron	N/A
	ENSG00000303770	ENST00000797092.1		n.84-5906T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96786 AN: 151786 Hom.: 31709 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.638 AC: 96913 AN: 151904 Hom.: 31768 Cov.: 32 AF XY: 0.639 AC XY: 47451 AN XY: 74230

African (AFR) AF: 0.796 AC: 33020 AN: 41464

American (AMR) AF: 0.640 AC: 9760 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2056 AN: 3466

East Asian (EAS) AF: 0.676 AC: 3480 AN: 5146

South Asian (SAS) AF: 0.570 AC: 2747 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6259 AN: 10548

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37738 AN: 67908

Other (OTH) AF: 0.639 AC: 1346 AN: 2106

Alfa AF: 0.593 Hom.: 3390

Bravo AF: 0.646

Asia WGS AF: 0.652 AC: 2263 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.85
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1921649; hg19: chr2-224269190;