rs366839

chr1-189589536-G-A

Variant summary

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

The XR_002958413.2(LOC105371657):n.550-13947G>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 0.551 in 151,818 control chromosomes in the GnomAD database, including 23,972 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 0.55 (23972 hom., cov: 31)
• Consequence: LOC105371657 XR_002958413.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

LOC105371657 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371657	XR_002958413.2	n.550-13947G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83532 AN: 151700 Hom.: 23941 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.551 AC: 83609 AN: 151818 Hom.: 23972 Cov.: 31 AF XY: 0.546 AC XY: 40503 AN XY: 74176

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.522

Alfa AF: 0.496 Hom.: 18687

Bravo AF: 0.553

Asia WGS AF: 0.441 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.28
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: rs366839; hg19: chr1-189558666; COSMIC: COSV60002297;