rs1549050

chr18-29188221-C-Achr18-29188221-C-T

Variant summary

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

The XR_935327.3(LOC105372044):n.281-6327G>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 0.917 in 152,066 control chromosomes in the GnomAD database, including 64,371 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 0.92 (64371 hom., cov: 32)
• Consequence: LOC105372044 XR_935327.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716

Genes affected

LOC105372044 (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 = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372044	XR_935327.3	n.281-6327G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139390 AN: 151948 Hom.: 64333 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.917 AC: 139480 AN: 152066 Hom.: 64371 Cov.: 32 AF XY: 0.920 AC XY: 68425 AN XY: 74338

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.979

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.937

Alfa AF: 0.944 Hom.: 33899

Bravo AF: 0.911

Asia WGS AF: 0.979 AC: 3405 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	3.2
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1549050; hg19: chr18-26768186;