rs873348

Variant names:

• chr4-176950206-G-A
• rs873348
• ENST00000656694.1:n.347-56301C>T

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.347-56301C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,196 control chromosomes in the GnomAD database, including 2,997 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 0.17 (2997 hom., cov: 33)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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
ENSG00000287544	ENST00000656694.1	n.347-56301C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26028 AN: 152078 Hom.: 2978 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.171 AC: 26080 AN: 152196 Hom.: 2997 Cov.: 33 AF XY: 0.170 AC XY: 12658 AN XY: 74390

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.156

Alfa AF: 0.151 Hom.: 364

Bravo AF: 0.182

Asia WGS AF: 0.0850 AC: 297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873348; hg19: chr4-177871360;