XR_947057.3:n.1137T>C

Variant names:

• chr1-22173037-T-C
• rs17360053
• XR_947057.3:n.1137T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

LOC105376850 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725701.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294752	ENST00000725701.1		n.301+807T>C		intron	N/A
	ENSG00000294752	ENST00000725702.1		n.125+9541T>C		intron	N/A
	ENSG00000294752	ENST00000725703.1		n.108+9541T>C		intron	N/A

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

African (AFR) AF: 0.173 AC: 7194 AN: 41502

American (AMR) AF: 0.241 AC: 3685 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1008 AN: 5170

South Asian (SAS) AF: 0.278 AC: 1339 AN: 4812

European-Finnish (FIN) AF: 0.357 AC: 3774 AN: 10564

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25126 AN: 67970

Other (OTH) AF: 0.314 AC: 662 AN: 2106

Alfa AF: 0.336 Hom.: 29084

Bravo AF: 0.278

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.72
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs17360053; hg19: chr1-22499530;