rs4795080

Variant names:

• chr17-27808608-T-A
• rs4795080
• ENST00000582441.1:c.220-4267A>T

Your query was ambiguous. Multiple possible variants found:

• chr17-27808608-T-A
• chr17-27808608-T-G

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-4267A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,138 control chromosomes in the GnomAD database, including 6,471 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 0.29 (6471 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 6 publications found

Genes affected

ENSG00000266202 (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 (AMR) allele frequency at 95% confidence interval = 0.353 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
ENSG00000266202	ENST00000582441.1	c.220-4267A>T		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43752 AN: 152018 Hom.: 6458 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.288 AC: 43803 AN: 152138 Hom.: 6471 Cov.: 32 AF XY: 0.292 AC XY: 21737 AN XY: 74366

African (AFR) AF: 0.269 AC: 11145 AN: 41502

American (AMR) AF: 0.360 AC: 5512 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1406 AN: 5166

South Asian (SAS) AF: 0.347 AC: 1672 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3285 AN: 10596

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18918 AN: 67976

Other (OTH) AF: 0.275 AC: 581 AN: 2114

Alfa AF: 0.161 Hom.: 325

Bravo AF: 0.288

Asia WGS AF: 0.330 AC: 1147 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	1.2
DANN	Benign	0.71
PhyloP100		-0.19

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4795080; hg19: chr17-26135634;