rs1469344

Positions:

• chr1-54920494-C-T

Variant summary

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

The ENST00000689429.1(ENSG00000242396):​n.324+33359C>T 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 0.242 in 152,036 control chromosomes in the GnomAD database, including 5,128 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 0.24 (5128 hom., cov: 31)
• Consequence: ENST00000689429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.74

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904184	XR_007066103.1	n.132+11636C>T		intron_variant, non_coding_transcript_variant
LOC124904184	XR_007066101.1	n.132+11636C>T		intron_variant, non_coding_transcript_variant
LOC124904184	XR_007066102.1	n.133-5124C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689429.1	n.324+33359C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36832 AN: 151918 Hom.: 5132 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.242 AC: 36822 AN: 152036 Hom.: 5128 Cov.: 31 AF XY: 0.240 AC XY: 17818 AN XY: 74324

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.0677

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.258

Alfa AF: 0.290 Hom.: 3956

Bravo AF: 0.233

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.012
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: rs1469344; hg19: chr1-55386167;