5-159307509-T-C

Variant names:

• chr5-159307509-T-C
• rs11135058
• ENST00000765301.1:n.221+2948A>G

Variant summary

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

The ENST00000765301.1(ENSG00000299638):​n.221+2948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,006 control chromosomes in the GnomAD database, including 24,292 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 0.56 (24292 hom., cov: 31)
• Consequence: ENSG00000299638 ENST00000765301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 5 publications found

Genes affected

ENSG00000299638 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 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
ENSG00000299638	ENST00000765301.1	n.221+2948A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85047 AN: 151888 Hom.: 24243 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.560 AC: 85148 AN: 152006 Hom.: 24292 Cov.: 31 AF XY: 0.562 AC XY: 41750 AN XY: 74306

African (AFR) AF: 0.652 AC: 27017 AN: 41434

American (AMR) AF: 0.616 AC: 9409 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1949 AN: 3464

East Asian (EAS) AF: 0.676 AC: 3495 AN: 5168

South Asian (SAS) AF: 0.546 AC: 2627 AN: 4812

European-Finnish (FIN) AF: 0.497 AC: 5251 AN: 10574

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33557 AN: 67962

Other (OTH) AF: 0.608 AC: 1285 AN: 2114

Alfa AF: 0.540 Hom.: 9658

Bravo AF: 0.580

Asia WGS AF: 0.658 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.016
DANN	Benign	0.52
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11135058; hg19: chr5-158734517;