chr7-128196079-G-A

Variant names:

• chr7-128196079-G-A
• rs4731413
• ENST00000710955.1:n.306-9610G>A

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.306-9610G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,152 control chromosomes in the GnomAD database, including 1,952 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 0.14 (1952 hom., cov: 32)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 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.306-9610G>A		intron_variant	Intron 1 of 3
ENSG00000292309	ENST00000765690.1	n.233-9604G>A		intron_variant	Intron 2 of 4
ENSG00000292309	ENST00000765691.1	n.142-9604G>A		intron_variant	Intron 1 of 3
ENSG00000292309	ENST00000765692.1	n.190-5556G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21525 AN: 152034 Hom.: 1952 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.141 AC: 21522 AN: 152152 Hom.: 1952 Cov.: 32 AF XY: 0.135 AC XY: 10069 AN XY: 74374

African (AFR) AF: 0.0401 AC: 1664 AN: 41514

American (AMR) AF: 0.157 AC: 2393 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3468

East Asian (EAS) AF: 0.0310 AC: 161 AN: 5186

South Asian (SAS) AF: 0.100 AC: 484 AN: 4816

European-Finnish (FIN) AF: 0.142 AC: 1506 AN: 10572

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13915 AN: 67994

Other (OTH) AF: 0.174 AC: 367 AN: 2112

Alfa AF: 0.171 Hom.: 1109

Bravo AF: 0.139

Asia WGS AF: 0.0730 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.61
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs4731413; hg19: chr7-127836132;