1-232948998-T-C

Position:

• chr1-232948998-T-C

Variant summary

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

The XR_001738525.2(LOC107985361):​n.2381A>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 0.243 in 152,126 control chromosomes in the GnomAD database, including 4,589 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 (4589 hom., cov: 32)
• Consequence: LOC107985361 XR_001738525.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

LOC107985361 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985361	XR_001738525.2	n.2381A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36900 AN: 152008 Hom.: 4569 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.243 AC: 36966 AN: 152126 Hom.: 4589 Cov.: 32 AF XY: 0.240 AC XY: 17837 AN XY: 74350

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.246

Alfa AF: 0.233 Hom.: 8586

Bravo AF: 0.245

Asia WGS AF: 0.240 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3820124; hg19: chr1-233084744;