rs1508147

Variant names:

• chr17-78226507-G-A
• rs1508147
• ENST00000835545.1:n.352-5432C>T

Variant summary

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

The ENST00000835545.1(ENSG00000308650):​n.352-5432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,114 control chromosomes in the GnomAD database, including 11,036 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 0.38 (11036 hom., cov: 33)
• Consequence: ENSG00000308650 ENST00000835545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 10 publications found

Genes affected

ENSG00000308650 (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 (SAS) allele frequency at 95% confidence interval = 0.423 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
ENSG00000308650	ENST00000835545.1	n.352-5432C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57764 AN: 151996 Hom.: 11026 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.380 AC: 57816 AN: 152114 Hom.: 11036 Cov.: 33 AF XY: 0.380 AC XY: 28249 AN XY: 74350

African (AFR) AF: 0.383 AC: 15904 AN: 41480

American (AMR) AF: 0.407 AC: 6225 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1971 AN: 5166

South Asian (SAS) AF: 0.438 AC: 2114 AN: 4824

European-Finnish (FIN) AF: 0.349 AC: 3686 AN: 10564

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25323 AN: 68010

Other (OTH) AF: 0.387 AC: 815 AN: 2108

Alfa AF: 0.380 Hom.: 6263

Bravo AF: 0.382

Asia WGS AF: 0.391 AC: 1361 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	0.0020
DANN	Benign	0.54
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1508147; hg19: chr17-76222588;