chr7-128202756-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000292309	ENST00000710955.1	n.306-2933A>G		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0800

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.165

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4577902; hg19: chr7-127842809;