ENST00000795667.1:n.164-5478C>T

Variant names:

• chr4-182888119-C-T
• rs17271644
• ENST00000795667.1:n.164-5478C>T

Variant summary

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

The ENST00000795667.1(ENSG00000303565):​n.164-5478C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,844 control chromosomes in the GnomAD database, including 20,516 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 0.50 (20516 hom., cov: 31)
• Consequence: ENSG00000303565 ENST00000795667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 3 publications found

Genes affected

ENSG00000303565 (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 = 0.705 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
ENSG00000303565	ENST00000795667.1	n.164-5478C>T		intron_variant	Intron 1 of 3
ENSG00000303565	ENST00000795668.1	n.305-5481C>T		intron_variant	Intron 1 of 2
ENSG00000303565	ENST00000795669.1	n.349-5481C>T		intron_variant	Intron 1 of 1
ENSG00000303565	ENST00000795670.1	n.335-2917C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76390 AN: 151726 Hom.: 20500 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.503 AC: 76452 AN: 151844 Hom.: 20516 Cov.: 31 AF XY: 0.501 AC XY: 37153 AN XY: 74194

African (AFR) AF: 0.712 AC: 29488 AN: 41428

American (AMR) AF: 0.433 AC: 6598 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2137 AN: 5142

South Asian (SAS) AF: 0.510 AC: 2449 AN: 4802

European-Finnish (FIN) AF: 0.406 AC: 4270 AN: 10526

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28830 AN: 67912

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.446 Hom.: 57010

Bravo AF: 0.514

Asia WGS AF: 0.485 AC: 1688 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	1.9
DANN	Benign	0.52
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs17271644; hg19: chr4-183809272;