rs2102317

chr4-125862569-A-C

Variant summary

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

The ENST00000667497.1(ENSG00000250149):n.163+109903A>C 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 0.805 in 151,982 control chromosomes in the GnomAD database, including 49,934 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 0.81 (49934 hom., cov: 31)
• Consequence: ENST00000667497.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 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
	ENST00000667497.1	n.163+109903A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122337 AN: 151866 Hom.: 49906 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.805 AC: 122416 AN: 151982 Hom.: 49934 Cov.: 31 AF XY: 0.801 AC XY: 59520 AN XY: 74278

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.800

Alfa AF: 0.848 Hom.: 25034

Bravo AF: 0.793

Asia WGS AF: 0.580 AC: 2019 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.8
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102317; hg19: chr4-126783724;