rs6429264

Positions:

• chr1-241359175-C-T

Variant summary

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

The XR_007067052.1(LOC124904601):​n.1584C>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 0.149 in 151,902 control chromosomes in the GnomAD database, including 1,890 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 0.15 (1890 hom., cov: 31)
• Consequence: LOC124904601 XR_007067052.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

Genes affected

LOC124904601 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904601	XR_007067052.1	n.1584C>T		non_coding_transcript_exon_variant	2/2
LOC124904601	XR_007067051.1	n.351+1233C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670763.1	n.141-1281C>T		intron_variant, non_coding_transcript_variant
	ENST00000655863.1	n.1413C>T		non_coding_transcript_exon_variant	2/2
	ENST00000655181.1	n.21+1693C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22602 AN: 151782 Hom.: 1886 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.149 AC: 22615 AN: 151902 Hom.: 1890 Cov.: 31 AF XY: 0.150 AC XY: 11136 AN XY: 74208

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.136

Alfa AF: 0.121 Hom.: 1325

Bravo AF: 0.161

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6429264; hg19: chr1-241522475;