rs12140275

Positions:

• chr1-38168207-A-T

Variant summary

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

The XR_001737985.1(LOC105378654):​n.62-24798A>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 0.211 in 151,948 control chromosomes in the GnomAD database, including 3,654 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 0.21 (3654 hom., cov: 31)
• Consequence: LOC105378654 XR_001737985.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

LOC105378654 (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 (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378654	XR_001737985.1	n.62-24798A>T		intron_variant, non_coding_transcript_variant
LOC105378654	XR_001737986.1	n.175+6384A>T		intron_variant, non_coding_transcript_variant
LOC105378654	XR_001737987.2	n.175+6384A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32100 AN: 151832 Hom.: 3650 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.211 AC: 32116 AN: 151948 Hom.: 3654 Cov.: 31 AF XY: 0.211 AC XY: 15678 AN XY: 74238

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.0126

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.221

Alfa AF: 0.223 Hom.: 496

Bravo AF: 0.198

Asia WGS AF: 0.118 AC: 413 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12140275; hg19: chr1-38633879;