7-128237160-A-G

Variant names:

• chr7-128237160-A-G
• rs1349419
• ENST00000785131.1:n.169-15620T>C

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-15620T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,054 control chromosomes in the GnomAD database, including 17,654 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 0.44 (17654 hom., cov: 32)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 13 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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	ENST00000785131.1	n.169-15620T>C		intron_variant	Intron 1 of 1
ENSG00000289434	ENST00000690022.2	n.-137T>C		upstream_gene_variant
ENSG00000289434	ENST00000692614.3	n.-86T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66459 AN: 151936 Hom.: 17650 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.437 AC: 66459 AN: 152054 Hom.: 17654 Cov.: 32 AF XY: 0.445 AC XY: 33066 AN XY: 74324

African (AFR) AF: 0.118 AC: 4896 AN: 41498

American (AMR) AF: 0.509 AC: 7775 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3468

East Asian (EAS) AF: 0.746 AC: 3856 AN: 5172

South Asian (SAS) AF: 0.602 AC: 2906 AN: 4826

European-Finnish (FIN) AF: 0.561 AC: 5912 AN: 10536

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37547 AN: 67968

Other (OTH) AF: 0.469 AC: 992 AN: 2114

Alfa AF: 0.417 Hom.: 2357

Bravo AF: 0.416

Asia WGS AF: 0.648 AC: 2249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs1349419; hg19: chr7-127877213;