rs7240405

Positions:

• chr18-49632720-A-G
• chr18-49632720-A-T

Variant summary

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

The XR_007066363.1(LOC105372112):​n.178+19851A>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 0.858 in 152,238 control chromosomes in the GnomAD database, including 56,108 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 0.86 (56108 hom., cov: 33)
• Consequence: LOC105372112 XR_007066363.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

Genes affected

LOC105372112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372112	XR_007066363.1	n.178+19851A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130498 AN: 152120 Hom.: 56062 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.858 AC: 130602 AN: 152238 Hom.: 56108 Cov.: 33 AF XY: 0.861 AC XY: 64082 AN XY: 74432

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.867

Alfa AF: 0.846 Hom.: 66442

Bravo AF: 0.864

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.74
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7240405; hg19: chr18-47159090;