rs884329

chr4-105002314-T-C

Variant summary

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

The ENST00000671069.1(ENSG00000248373):n.636+32967T>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 0.338 in 151,960 control chromosomes in the GnomAD database, including 10,350 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 0.34 (10350 hom., cov: 30)
• Consequence: ENST00000671069.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.443 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
	ENST00000671069.1	n.636+32967T>C		intron_variant, non_coding_transcript_variant
	ENST00000506148.5	n.207+32967T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000506386.1	n.71+28532T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51370 AN: 151842 Hom.: 10349 Cov.: 30

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.0797

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.338 AC: 51370 AN: 151960 Hom.: 10350 Cov.: 30 AF XY: 0.339 AC XY: 25154 AN XY: 74270

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.0799

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.385

Alfa AF: 0.364 Hom.: 2201

Bravo AF: 0.316

Asia WGS AF: 0.258 AC: 896 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.5
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884329; hg19: chr4-105923471;