rs4659485

Variant names:

• chr1-236982618-T-C
• rs4659485
• XR_007066964.1:n.392T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007066964.1(LOC124904563):​n.392T>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 0.398 in 151,998 control chromosomes in the GnomAD database, including 14,820 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 0.40 (14820 hom., cov: 32)
• Consequence: LOC124904563 XR_007066964.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 4 publications found

Genes affected

LOC124904563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904563	XR_007066964.1	n.392T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302268	ENST00000785366.1	n.336+195T>C		intron_variant	Intron 2 of 2
ENSG00000302268	ENST00000785367.1	n.210+195T>C		intron_variant	Intron 2 of 2
ENSG00000302268	ENST00000785368.1	n.151+195T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60561 AN: 151880 Hom.: 14818 Cov.: 32

Gnomad AFR AF: 0.0979

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.398 AC: 60563 AN: 151998 Hom.: 14820 Cov.: 32 AF XY: 0.400 AC XY: 29750 AN XY: 74288

African (AFR) AF: 0.0976 AC: 4050 AN: 41478

American (AMR) AF: 0.447 AC: 6813 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2741 AN: 5158

South Asian (SAS) AF: 0.551 AC: 2651 AN: 4810

European-Finnish (FIN) AF: 0.519 AC: 5476 AN: 10542

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35702 AN: 67964

Other (OTH) AF: 0.411 AC: 869 AN: 2114

Alfa AF: 0.453 Hom.: 2939

Bravo AF: 0.379

Asia WGS AF: 0.490 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.3
DANN	Benign	0.71
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs4659485; hg19: chr1-237145918;