rs4892122

chr18-73655487-G-A

Variant summary

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

The XR_007066468.1(LOC105372190):n.64-84C>T 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 0.695 in 152,128 control chromosomes in the GnomAD database, including 36,746 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 0.69 (36746 hom., cov: 33)
• Consequence: LOC105372190 XR_007066468.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

LOC105372190 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372190	XR_007066468.1	n.64-84C>T		intron_variant, non_coding_transcript_variant
LOC105372190	XR_007066469.1	n.171-84C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105584 AN: 152010 Hom.: 36725 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.695 AC: 105658 AN: 152128 Hom.: 36746 Cov.: 33 AF XY: 0.697 AC XY: 51854 AN XY: 74366

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.685

Alfa AF: 0.685 Hom.: 4844

Bravo AF: 0.698

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.2
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4892122; hg19: chr18-71322722;