rs1625040

Positions:

• chr1-236983079-A-G
• chr1-236983079-A-T

Variant summary

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

The XR_001738551.1(LOC107985368):​n.23A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 152,246 control chromosomes in the GnomAD database, including 54,685 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 (54685 hom., cov: 33)
• Consequence: LOC107985368 XR_001738551.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

LOC107985368 (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 (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985368	XR_001738551.1	n.23A>G		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128686 AN: 152126 Hom.: 54622 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.846 AC: 128809 AN: 152246 Hom.: 54685 Cov.: 33 AF XY: 0.850 AC XY: 63259 AN XY: 74428

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.928

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.807

Alfa AF: 0.854 Hom.: 6913

Bravo AF: 0.839

Asia WGS AF: 0.910 AC: 3167 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	4.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1625040; hg19: chr1-237146379;