rs1438676

Positions:

• chr5-110972184-T-C

Variant summary

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

The ENST00000507627.1(ENSG00000248428):​n.483-1019A>G 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 0.246 in 152,104 control chromosomes in the GnomAD database, including 8,118 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 0.25 (8118 hom., cov: 33)
• Consequence: ENST00000507627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507627.1	n.483-1019A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37274 AN: 151986 Hom.: 8083 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.0886

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0831

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.246 AC: 37377 AN: 152104 Hom.: 8118 Cov.: 33 AF XY: 0.245 AC XY: 18184 AN XY: 74368

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.0886

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0831

Gnomad4 OTH AF: 0.225

Alfa AF: 0.128 Hom.: 1150

Bravo AF: 0.267

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
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: rs1438676; hg19: chr5-110307883;