chr1-173489667-C-T

Position:

• chr1-173489667-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007066738.1(LOC124904456):​n.3140G>A 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 0.0116 in 129,994 control chromosomes in the GnomAD database, including 11 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 0.012 (11 hom., cov: 26)
• Consequence: LOC124904456 XR_007066738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

LOC124904456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0116 (1514/129994) while in subpopulation NFE AF= 0.0172 (1117/64792). AF 95% confidence interval is 0.0164. There are 11 homozygotes in gnomad4. There are 677 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904456	XR_007066738.1	n.3140G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0117 AC: 1514 AN: 129914 Hom.: 11 Cov.: 26

Gnomad AFR AF: 0.00307

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00786

Gnomad ASJ AF: 0.00982

Gnomad EAS AF: 0.000269

Gnomad SAS AF: 0.00456

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.00526

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0116 AC: 1514 AN: 129994 Hom.: 11 Cov.: 26 AF XY: 0.0111 AC XY: 677 AN XY: 61202

Gnomad4 AFR AF: 0.00306

Gnomad4 AMR AF: 0.00785

Gnomad4 ASJ AF: 0.00982

Gnomad4 EAS AF: 0.000270

Gnomad4 SAS AF: 0.00456

Gnomad4 FIN AF: 0.0203

Gnomad4 NFE AF: 0.0172

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0143 Hom.: 7

Bravo AF: 0.00880

Asia WGS AF: 0.00145 AC: 5 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35358649; hg19: chr1-173458806;