rs873348

Positions:

• chr4-176950206-G-A

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, non coding transcript 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: ENST00000656694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656694.1	n.347-56301C>T		intron_variant, non_coding_transcript_variant

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;