ENST00000741164.1:n.429-6517G>C

Variant names:

• chr7-4528374-G-C
• rs975926
• ENST00000741164.1:n.429-6517G>C

Variant summary

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

The ENST00000741164.1(ENSG00000296681):​n.429-6517G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,880 control chromosomes in the GnomAD database, including 27,473 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 0.58 (27473 hom., cov: 30)
• Consequence: ENSG00000296681 ENST00000741164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 0 publications found

Genes affected

ENSG00000296681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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
ENSG00000296681	ENST00000741164.1	n.429-6517G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87565 AN: 151762 Hom.: 27413 Cov.: 30

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.577 AC: 87685 AN: 151880 Hom.: 27473 Cov.: 30 AF XY: 0.584 AC XY: 43335 AN XY: 74192

African (AFR) AF: 0.814 AC: 33699 AN: 41422

American (AMR) AF: 0.656 AC: 10014 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3289 AN: 5136

South Asian (SAS) AF: 0.614 AC: 2957 AN: 4814

European-Finnish (FIN) AF: 0.489 AC: 5150 AN: 10542

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29069 AN: 67928

Other (OTH) AF: 0.566 AC: 1194 AN: 2110

Alfa AF: 0.505 Hom.: 2600

Bravo AF: 0.600

Asia WGS AF: 0.661 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.33
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs975926; hg19: chr7-4568005;