chr5-159304540-G-A

Variant names:

• chr5-159304540-G-A
• rs1549922
• ENST00000765301.1:n.222-1848C>T

Variant summary

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

The ENST00000765301.1(ENSG00000299638):​n.222-1848C>T 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 151,986 control chromosomes in the GnomAD database, including 24,276 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 (24276 hom., cov: 31)
• Consequence: ENSG00000299638 ENST00000765301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 10 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765301.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299638	ENST00000765301.1		n.222-1848C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85029 AN: 151866 Hom.: 24228 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.560 AC: 85130 AN: 151986 Hom.: 24276 Cov.: 31 AF XY: 0.562 AC XY: 41734 AN XY: 74270

African (AFR) AF: 0.652 AC: 27011 AN: 41440

American (AMR) AF: 0.615 AC: 9400 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3496 AN: 5172

South Asian (SAS) AF: 0.546 AC: 2627 AN: 4814

European-Finnish (FIN) AF: 0.498 AC: 5251 AN: 10550

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

European-Non Finnish (NFE) AF: 0.494 AC: 33555 AN: 67950

Other (OTH) AF: 0.607 AC: 1282 AN: 2112

Alfa AF: 0.539 Hom.: 8589

Bravo AF: 0.580

Asia WGS AF: 0.658 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.59
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1549922; hg19: chr5-158731548;