rs4921466

Variant names:

• chr5-159305764-T-C
• rs4921466
• ENST00000765301.1:n.222-3072A>G

Variant summary

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

The ENST00000765301.1(ENSG00000299638):​n.222-3072A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,208 control chromosomes in the GnomAD database, including 885 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 0.11 (885 hom., cov: 32)
• Consequence: ENSG00000299638 ENST00000765301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 11 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.124 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299638	ENST00000765301.1		n.222-3072A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16034 AN: 152090 Hom.: 880 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.105 AC: 16054 AN: 152208 Hom.: 885 Cov.: 32 AF XY: 0.102 AC XY: 7599 AN XY: 74442

African (AFR) AF: 0.107 AC: 4439 AN: 41486

American (AMR) AF: 0.129 AC: 1970 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3472

East Asian (EAS) AF: 0.0594 AC: 308 AN: 5186

South Asian (SAS) AF: 0.0647 AC: 312 AN: 4820

European-Finnish (FIN) AF: 0.0711 AC: 755 AN: 10612

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7234 AN: 68020

Other (OTH) AF: 0.119 AC: 252 AN: 2114

Alfa AF: 0.114 Hom.: 216

Bravo AF: 0.114

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs4921466; hg19: chr5-158732772;