ENST00000710955.1:n.306-2933A>G

Variant names:

• chr7-128202756-A-G
• rs4577902
• ENST00000710955.1:n.306-2933A>G

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-2933A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 151,950 control chromosomes in the GnomAD database, including 2,838 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 0.17 (2838 hom., cov: 32)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 2 publications found

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000710955.1. 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
	ENSG00000292309	ENST00000710955.1		n.306-2933A>G		intron	N/A
	ENSG00000292309	ENST00000765690.1		n.233-2927A>G		intron	N/A
	ENSG00000292309	ENST00000765691.1		n.142-2927A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25141 AN: 151832 Hom.: 2824 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0800

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.166 AC: 25194 AN: 151950 Hom.: 2838 Cov.: 32 AF XY: 0.163 AC XY: 12126 AN XY: 74268

African (AFR) AF: 0.327 AC: 13529 AN: 41408

American (AMR) AF: 0.0928 AC: 1418 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3472

East Asian (EAS) AF: 0.164 AC: 841 AN: 5140

South Asian (SAS) AF: 0.127 AC: 609 AN: 4812

European-Finnish (FIN) AF: 0.0800 AC: 846 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7036 AN: 67950

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.138 Hom.: 259

Bravo AF: 0.174

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.2
DANN	Benign	0.87
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4577902; hg19: chr7-127842809;