rs2029118

Variant names:

• chr3-54114743-G-A
• rs2029118
• ENST00000666932.2:n.1187+8314C>T

Variant summary

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

The ENST00000666932.2(ENSG00000286353):​n.1187+8314C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 152,194 control chromosomes in the GnomAD database, including 849 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 0.096 (849 hom., cov: 32)
• Consequence: ENSG00000286353 ENST00000666932.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 4 publications found

Genes affected

ENSG00000286353 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909381	XR_007095914.1	n.386+8314C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286353	ENST00000666932.2	n.1187+8314C>T		intron_variant	Intron 2 of 2
ENSG00000286353	ENST00000790844.1	n.394+8314C>T		intron_variant	Intron 1 of 3
ENSG00000286353	ENST00000790845.1	n.386+8314C>T		intron_variant	Intron 1 of 3
ENSG00000286353	ENST00000790846.1	n.386+8314C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14559 AN: 152074 Hom.: 847 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0651

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0957 AC: 14565 AN: 152194 Hom.: 849 Cov.: 32 AF XY: 0.0976 AC XY: 7258 AN XY: 74394

African (AFR) AF: 0.158 AC: 6569 AN: 41496

American (AMR) AF: 0.105 AC: 1598 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3470

East Asian (EAS) AF: 0.106 AC: 548 AN: 5172

South Asian (SAS) AF: 0.0648 AC: 312 AN: 4816

European-Finnish (FIN) AF: 0.0869 AC: 922 AN: 10604

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0576 AC: 3916 AN: 68030

Other (OTH) AF: 0.0876 AC: 185 AN: 2112

Alfa AF: 0.0703 Hom.: 827

Bravo AF: 0.0976

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2029118; hg19: chr3-54148770;