rs346923

Variant names:

• chr4-52545963-G-A
• rs346923
• ENST00000660768.1:n.102+5510C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660768.1(ENSG00000287999):​n.102+5510C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,066 control chromosomes in the GnomAD database, including 4,436 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 0.20 (4436 hom., cov: 32)
• Consequence: ENSG00000287999 ENST00000660768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

ENSG00000287999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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
ENSG00000287999	ENST00000660768.1	n.102+5510C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30548 AN: 151948 Hom.: 4413 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.201 AC: 30626 AN: 152066 Hom.: 4436 Cov.: 32 AF XY: 0.197 AC XY: 14635 AN XY: 74326

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0799

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.196

Alfa AF: 0.130 Hom.: 2449

Bravo AF: 0.216

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346923; hg19: chr4-53412129;