7-128204042-A-G

Variant names:

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

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-1647A>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
• Publications: 5 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=-0.97).
• 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
ENSG00000292309	ENST00000765690.1	n.233-1641A>G		intron_variant	Intron 2 of 4
ENSG00000292309	ENST00000765691.1	n.142-1641A>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

African (AFR) AF: 0.849 AC: 35219 AN: 41506

American (AMR) AF: 0.796 AC: 12163 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3011 AN: 3470

East Asian (EAS) AF: 0.908 AC: 4678 AN: 5152

South Asian (SAS) AF: 0.809 AC: 3886 AN: 4806

European-Finnish (FIN) AF: 0.930 AC: 9855 AN: 10602

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62354 AN: 68014

Other (OTH) AF: 0.879 AC: 1854 AN: 2110

Alfa AF: 0.892 Hom.: 55610

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4731416; hg19: chr7-127844095;