chr18-10321350-A-G

Variant names:

• chr18-10321350-A-G
• rs206626
• XR_001753345.2:n.653T>C

Variant summary

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

The XR_001753345.2(LOC105371985):​n.653T>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 0.439 in 152,028 control chromosomes in the GnomAD database, including 17,016 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 0.44 (17016 hom., cov: 32)
• Consequence: LOC105371985 XR_001753345.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 2 publications found

Genes affected

LOC105371985 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371985	XR_001753345.2	n.653T>C		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105371985	XR_007066287.1	n.552T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105371985	XR_001753344.2	n.532+798T>C		intron_variant	Intron 3 of 4
LOC105371985	XR_001753346.2	n.463+798T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287065	ENST00000669383.1	n.401-1673A>G		intron_variant	Intron 2 of 2
ENSG00000287065	ENST00000826388.1	n.214-1673A>G		intron_variant	Intron 2 of 2
ENSG00000287065	ENST00000826389.1	n.135-1673A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66785 AN: 151910 Hom.: 17017 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.439 AC: 66792 AN: 152028 Hom.: 17016 Cov.: 32 AF XY: 0.442 AC XY: 32869 AN XY: 74294

African (AFR) AF: 0.162 AC: 6739 AN: 41502

American (AMR) AF: 0.550 AC: 8407 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2021 AN: 3468

East Asian (EAS) AF: 0.683 AC: 3530 AN: 5166

South Asian (SAS) AF: 0.432 AC: 2071 AN: 4796

European-Finnish (FIN) AF: 0.540 AC: 5688 AN: 10542

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36738 AN: 67954

Other (OTH) AF: 0.476 AC: 1003 AN: 2108

Alfa AF: 0.498 Hom.: 6857

Bravo AF: 0.433

Asia WGS AF: 0.532 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.80
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs206626; hg19: chr18-10321347; COSMIC: COSV73862170;