rs230271

Positions:

• chr1-39824925-C-A

Variant summary

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

The XR_947221.3(LOC105378667):​n.287+493C>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 0.56 in 151,960 control chromosomes in the GnomAD database, including 25,666 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 0.56 (25666 hom., cov: 32)
• Consequence: LOC105378667 XR_947221.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579

Genes affected

LOC105378667 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378667	XR_947221.3	n.287+493C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84971 AN: 151842 Hom.: 25612 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.560 AC: 85081 AN: 151960 Hom.: 25666 Cov.: 32 AF XY: 0.558 AC XY: 41424 AN XY: 74260

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.523

Alfa AF: 0.465 Hom.: 22091

Bravo AF: 0.574

Asia WGS AF: 0.605 AC: 2105 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	0.56
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230271; hg19: chr1-40290597;