rs931850

Positions:

• chr18-63726600-C-T

Variant summary

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

The XR_007066401.1(LOC124904318):​n.165+661G>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 0.689 in 152,008 control chromosomes in the GnomAD database, including 36,516 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 (36516 hom., cov: 31)
• Consequence: LOC124904318 XR_007066401.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

LOC124904318 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904318	XR_007066401.1	n.165+661G>A		intron_variant, non_coding_transcript_variant
LOC124904318	XR_007066402.1	n.191+661G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104699 AN: 151890 Hom.: 36499 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.689 AC: 104762 AN: 152008 Hom.: 36516 Cov.: 31 AF XY: 0.692 AC XY: 51433 AN XY: 74310

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.682

Alfa AF: 0.714 Hom.: 17751

Bravo AF: 0.684

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931850; hg19: chr18-61393834;