7-128226060-G-T

Variant names:

• chr7-128226060-G-T
• rs791601
• ENST00000690022.2:n.289-4520C>A

Variant summary

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

The ENST00000690022.2(ENSG00000289434):​n.289-4520C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,978 control chromosomes in the GnomAD database, including 11,530 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 0.38 (11530 hom., cov: 31)
• Consequence: ENSG00000289434 ENST00000690022.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 3 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 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
ENSG00000289434	ENST00000690022.2	n.289-4520C>A		intron_variant	Intron 2 of 2
ENSG00000289434	ENST00000692614.3	n.528-4520C>A		intron_variant	Intron 2 of 2
ENSG00000289434	ENST00000785131.1	n.169-4520C>A		intron_variant	Intron 1 of 1
ENSG00000289434	ENST00000785132.1	n.477-4523C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57424 AN: 151860 Hom.: 11528 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.378 AC: 57450 AN: 151978 Hom.: 11530 Cov.: 31 AF XY: 0.381 AC XY: 28260 AN XY: 74268

African (AFR) AF: 0.274 AC: 11333 AN: 41422

American (AMR) AF: 0.376 AC: 5742 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1330 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3648 AN: 5182

South Asian (SAS) AF: 0.344 AC: 1658 AN: 4820

European-Finnish (FIN) AF: 0.447 AC: 4715 AN: 10550

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27636 AN: 67940

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.372 Hom.: 1383

Bravo AF: 0.367

Asia WGS AF: 0.528 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs791601; hg19: chr7-127866113;