rs2317951

chr1-54968975-G-A

Variant summary

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

The ENST00000689429.1(ENSG00000242396):n.325-4673G>A 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 0.315 in 152,042 control chromosomes in the GnomAD database, including 7,717 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 0.31 (7717 hom., cov: 32)
• Consequence: ENST00000689429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904184	XR_007066103.1	n.133-4673G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689429.1	n.325-4673G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47817 AN: 151924 Hom.: 7722 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.315 AC: 47835 AN: 152042 Hom.: 7717 Cov.: 32 AF XY: 0.313 AC XY: 23232 AN XY: 74310

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.315

Alfa AF: 0.340 Hom.: 18166

Bravo AF: 0.305

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.9
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317951; hg19: chr1-55434648;