rs1667255

Positions:

• chr18-31607316-A-C
• chr18-31607316-A-G
• chr18-31607316-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The XR_007066326.1(LOC124904277):​n.128+57T>G 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 0.476 in 151,374 control chromosomes in the GnomAD database, including 18,780 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.48 (18780 hom., cov: 30)
• Consequence: LOC124904277 XR_007066326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

LOC124904277 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 18-31607316-A-C is Benign according to our data. Variant chr18-31607316-A-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904277	XR_007066326.1	n.128+57T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71912 AN: 151258 Hom.: 18731 Cov.: 30

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.476 AC: 72030 AN: 151374 Hom.: 18780 Cov.: 30 AF XY: 0.471 AC XY: 34832 AN XY: 73888

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.483

Alfa AF: 0.396 Hom.: 25718

Bravo AF: 0.502

Asia WGS AF: 0.450 AC: 1570 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1667255; hg19: chr18-29187279;