rs17778257

Variant names:

• chr5-148825014-A-T
• rs17778257
• ENST00000798472.1:n.255-162A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000798472.1(ENSG00000303969):​n.255-162A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,210 control chromosomes in the GnomAD database, including 9,692 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 0.35 (9692 hom., cov: 33)
• Consequence: ENSG00000303969 ENST00000798472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 21 publications found

Genes affected

ENSG00000303969 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.384 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
ENSG00000303969	ENST00000798472.1	n.255-162A>T		intron_variant	Intron 2 of 4
ENSG00000303969	ENST00000798473.1	n.252-186A>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52855 AN: 152092 Hom.: 9678 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.347 AC: 52893 AN: 152210 Hom.: 9692 Cov.: 33 AF XY: 0.354 AC XY: 26360 AN XY: 74418

African (AFR) AF: 0.239 AC: 9904 AN: 41526

American (AMR) AF: 0.389 AC: 5951 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1435 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2040 AN: 5184

South Asian (SAS) AF: 0.399 AC: 1924 AN: 4826

European-Finnish (FIN) AF: 0.474 AC: 5015 AN: 10584

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25546 AN: 67996

Other (OTH) AF: 0.369 AC: 780 AN: 2116

Alfa AF: 0.362 Hom.: 1454

Bravo AF: 0.335

Asia WGS AF: 0.403 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs17778257; hg19: chr5-148204577;