1-189468052-T-C

Position:

• chr1-189468052-T-C

Variant summary

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

The XR_002958413.2(LOC105371657):​n.483-100277T>C 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 0.154 in 152,130 control chromosomes in the GnomAD database, including 2,380 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 0.15 (2380 hom., cov: 32)
• Consequence: LOC105371657 XR_002958413.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

LOC105371657 (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 = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371657	XR_002958413.2	n.483-100277T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23497 AN: 152014 Hom.: 2379 Cov.: 32

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.154 AC: 23494 AN: 152130 Hom.: 2380 Cov.: 32 AF XY: 0.153 AC XY: 11376 AN XY: 74376

Gnomad4 AFR AF: 0.0383

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0514

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.153

Alfa AF: 0.202 Hom.: 2237

Bravo AF: 0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3860306; hg19: chr1-189437182;