ENST00000738470.1:n.36+5316C>T

Variant names:

• chr6-83507449-G-A
• rs7753918
• ENST00000738470.1:n.36+5316C>T

Variant summary

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

The ENST00000738470.1(ENSG00000296350):​n.36+5316C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,130 control chromosomes in the GnomAD database, including 2,302 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 0.16 (2302 hom., cov: 32)
• Consequence: ENSG00000296350 ENST00000738470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 1 publications found

Genes affected

ENSG00000296350 (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 (AFR) allele frequency at 95% confidence interval = 0.262 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
ENSG00000296350	ENST00000738470.1	n.36+5316C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24374 AN: 152012 Hom.: 2297 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.160 AC: 24403 AN: 152130 Hom.: 2302 Cov.: 32 AF XY: 0.154 AC XY: 11484 AN XY: 74372

African (AFR) AF: 0.266 AC: 11035 AN: 41464

American (AMR) AF: 0.103 AC: 1580 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3470

East Asian (EAS) AF: 0.0258 AC: 134 AN: 5184

South Asian (SAS) AF: 0.0701 AC: 338 AN: 4824

European-Finnish (FIN) AF: 0.0851 AC: 900 AN: 10580

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9412 AN: 68000

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.144 Hom.: 2179

Bravo AF: 0.167

Asia WGS AF: 0.0690 AC: 239 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	0.74
DANN	Benign	0.40
PhyloP100		-0.060

Splicing

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

Other links and lift over

dbSNP: rs7753918; hg19: chr6-84217168;