rs2069084

chr1-234849241-G-Achr1-234849241-G-Cchr1-234849241-G-T

Variant summary

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

The ENST00000651370.1(ENSG00000286263):n.186-34765C>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 0.849 in 152,196 control chromosomes in the GnomAD database, including 55,256 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 0.85 (55256 hom., cov: 33)
• Consequence: ENST00000651370.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985365	XR_001738533.2	n.2740+21361C>T		intron_variant, non_coding_transcript_variant
LOC107985365	XR_001738534.2	n.841+21361C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651370.1	n.186-34765C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129202 AN: 152078 Hom.: 55227 Cov.: 33

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.849 AC: 129285 AN: 152196 Hom.: 55256 Cov.: 33 AF XY: 0.852 AC XY: 63357 AN XY: 74402

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.864

Alfa AF: 0.873 Hom.: 71667

Bravo AF: 0.844

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.6
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069084; hg19: chr1-234984988;