7-4458057-C-T

Variant names:

• chr7-4458057-C-T
• rs895710
• ENST00000741164.1:n.174+23535C>T

Variant summary

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

The ENST00000741164.1(ENSG00000296681):​n.174+23535C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,790 control chromosomes in the GnomAD database, including 8,075 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 0.31 (8075 hom., cov: 32)
• Consequence: ENSG00000296681 ENST00000741164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901579	XR_007060198.1	n.46-18103C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296681	ENST00000741164.1	n.174+23535C>T		intron_variant	Intron 1 of 2
ENSG00000296681	ENST00000741167.1	n.214+23535C>T		intron_variant	Intron 1 of 1
ENSG00000296681	ENST00000741168.1	n.255-18103C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46633 AN: 151672 Hom.: 8072 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.307 AC: 46640 AN: 151790 Hom.: 8075 Cov.: 32 AF XY: 0.310 AC XY: 22970 AN XY: 74182

African (AFR) AF: 0.140 AC: 5819 AN: 41486

American (AMR) AF: 0.323 AC: 4928 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1597 AN: 5140

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4810

European-Finnish (FIN) AF: 0.413 AC: 4338 AN: 10498

Middle Eastern (MID) AF: 0.469 AC: 136 AN: 290

European-Non Finnish (NFE) AF: 0.385 AC: 26141 AN: 67842

Other (OTH) AF: 0.324 AC: 685 AN: 2114

Alfa AF: 0.352 Hom.: 30806

Bravo AF: 0.290

Asia WGS AF: 0.290 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs895710; hg19: chr7-4497688;