rs2061450

Positions:

• chr18-63093579-G-A
• chr18-63093579-G-T

Variant summary

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

The XR_935570.3(LOC105372161):​n.516-2434G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,014 control chromosomes in the GnomAD database, including 6,604 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 0.28 (6604 hom., cov: 32)
• Consequence: LOC105372161 XR_935570.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

LOC105372161 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372161	XR_935570.3	n.516-2434G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43197 AN: 151896 Hom.: 6595 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.285 AC: 43250 AN: 152014 Hom.: 6604 Cov.: 32 AF XY: 0.288 AC XY: 21366 AN XY: 74316

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.255

Alfa AF: 0.229 Hom.: 2001

Bravo AF: 0.298

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2061450; hg19: chr18-60760812;