1-54968770-T-G

Variant summary

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

The ENST00000689429.1(ENSG00000242396):n.325-4878T>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 0.692 in 152,122 control chromosomes in the GnomAD database, including 36,660 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 0.69 (36660 hom., cov: 33)
• Consequence: ENST00000689429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904184	XR_007066103.1	n.133-4878T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689429.1	n.325-4878T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105129 AN: 152002 Hom.: 36625 Cov.: 33

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.692 AC: 105227 AN: 152122 Hom.: 36660 Cov.: 33 AF XY: 0.693 AC XY: 51487 AN XY: 74348

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.704

Alfa AF: 0.647 Hom.: 12722

Bravo AF: 0.703

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.21
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317948; hg19: chr1-55434443;