7-4474175-C-T

Variant names:

• chr7-4474175-C-T
• rs4720301
• ENST00000741164.1:n.175-13822C>T

Variant summary

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

The ENST00000741164.1(ENSG00000296681):​n.175-13822C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,754 control chromosomes in the GnomAD database, including 21,630 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 0.53 (21630 hom., cov: 31)
• Consequence: ENSG00000296681 ENST00000741164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901579	XR_007060198.1	n.46-1985C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296681	ENST00000741164.1	n.175-13822C>T		intron_variant	Intron 1 of 2
ENSG00000296681	ENST00000741167.1	n.215-13822C>T		intron_variant	Intron 1 of 1
ENSG00000296681	ENST00000741168.1	n.255-1985C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80812 AN: 151638 Hom.: 21602 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.533 AC: 80878 AN: 151754 Hom.: 21630 Cov.: 31 AF XY: 0.536 AC XY: 39699 AN XY: 74126

African (AFR) AF: 0.515 AC: 21326 AN: 41370

American (AMR) AF: 0.591 AC: 9010 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3466

East Asian (EAS) AF: 0.688 AC: 3507 AN: 5098

South Asian (SAS) AF: 0.563 AC: 2705 AN: 4804

European-Finnish (FIN) AF: 0.511 AC: 5378 AN: 10532

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.519 AC: 35260 AN: 67928

Other (OTH) AF: 0.536 AC: 1130 AN: 2110

Alfa AF: 0.524 Hom.: 12194

Bravo AF: 0.541

Asia WGS AF: 0.587 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.78
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4720301; hg19: chr7-4513806;