rs1943816

Positions:

• chr18-73391387-A-G

Variant summary

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

The XR_007066468.1(LOC105372190):​n.1384+9025T>C 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 0.173 in 151,780 control chromosomes in the GnomAD database, including 2,851 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 0.17 (2851 hom., cov: 32)
• Consequence: LOC105372190 XR_007066468.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

LOC105372190 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372190	XR_007066468.1	n.1384+9025T>C		intron_variant, non_coding_transcript_variant
LOC105372190	XR_007066469.1	n.1491+9025T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26232 AN: 151662 Hom.: 2845 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.173 AC: 26263 AN: 151780 Hom.: 2851 Cov.: 32 AF XY: 0.171 AC XY: 12696 AN XY: 74196

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0995

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.156

Alfa AF: 0.132 Hom.: 2122

Bravo AF: 0.178

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943816; hg19: chr18-71058622;