7-128204042-A-G

Variant names:

• chr7-128204042-A-G
• rs4731416
• ENST00000710955.1:n.306-1647A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000710955.1(ENSG00000292309):​n.306-1647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,148 control chromosomes in the GnomAD database, including 59,358 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 0.88 (59358 hom., cov: 31)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.911 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.306-1647A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134044 AN: 152030 Hom.: 59318 Cov.: 31

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.882 AC: 134138 AN: 152148 Hom.: 59358 Cov.: 31 AF XY: 0.878 AC XY: 65310 AN XY: 74366

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.879

Alfa AF: 0.893 Hom.: 37596

Bravo AF: 0.869

Asia WGS AF: 0.854 AC: 2969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731416; hg19: chr7-127844095;