rs17360053

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376850	XR_947057.3	n.1137T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294752	ENST00000725701.1	n.301+807T>C		intron_variant	Intron 2 of 3
ENSG00000294752	ENST00000725702.1	n.125+9541T>C		intron_variant	Intron 1 of 2
ENSG00000294752	ENST00000725703.1	n.108+9541T>C		intron_variant	Intron 1 of 3

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 v4.3

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;