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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741164.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296681	ENST00000741164.1		n.175-13822C>T		intron	N/A
	ENSG00000296681	ENST00000741167.1		n.215-13822C>T		intron	N/A
	ENSG00000296681	ENST00000741168.1		n.255-1985C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4720301;

hg19: chr7-4513806;