chr1-22173037-T-C

Position:

• chr1-22173037-T-C

Variant summary

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

The XR_947057.3(LOC105376850):​n.1137T>C 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 0.291 in 152,082 control chromosomes in the GnomAD database, including 7,082 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 0.29 (7082 hom., cov: 32)
• Consequence: LOC105376850 XR_947057.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

Genes affected

LOC105376850 (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 = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376850	XR_947057.3	n.1137T>C		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44235 AN: 151964 Hom.: 7074 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.291 AC: 44259 AN: 152082 Hom.: 7082 Cov.: 32 AF XY: 0.289 AC XY: 21508 AN XY: 74338

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.314

Alfa AF: 0.345 Hom.: 12963

Bravo AF: 0.278

Asia WGS AF: 0.275 AC: 957 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	0.55
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17360053; hg19: chr1-22499530;