rs35668979

chr1-1164430-C-T

Variant summary

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

The XR_007065348.1(LOC124903818):n.1178C>T 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 0.013 in 152,186 control chromosomes in the GnomAD database, including 35 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 0.013 (35 hom., cov: 32)
• Consequence: LOC124903818 XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

Genes affected

LOC124903818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.013 (1979/152186) while in subpopulation NFE AF= 0.0209 (1424/68000). AF 95% confidence interval is 0.02. There are 35 homozygotes in gnomad4. There are 877 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903818	XR_007065348.1	n.1178C>T		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0130 AC: 1979 AN: 152068 Hom.: 35 Cov.: 32

Gnomad AFR AF: 0.00362

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.00812

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00622

Gnomad FIN AF: 0.00415

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0130 AC: 1979 AN: 152186 Hom.: 35 Cov.: 32 AF XY: 0.0118 AC XY: 877 AN XY: 74410

Gnomad4 AFR AF: 0.00361

Gnomad4 AMR AF: 0.00811

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.00415

Gnomad4 NFE AF: 0.0209

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0170 Hom.: 3

Bravo AF: 0.0134

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	9.6
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35668979; hg19: chr1-1099810;