chr1-39824925-C-A

Variant names:

• chr1-39824925-C-A
• rs230271
• XR_947221.3:n.287+493C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_947221.3(LOC105378667):​n.287+493C>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 7 publications found

Genes affected

LOC105378667 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780948.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301696	ENST00000780948.1		n.-196C>A		upstream_gene	N/A
	ENSG00000301696	ENST00000780949.1		n.-224C>A		upstream_gene	N/A
	ENSG00000301696	ENST00000780950.1		n.-233C>A		upstream_gene	N/A

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

African (AFR) AF: 0.802 AC: 33230 AN: 41452

American (AMR) AF: 0.493 AC: 7533 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3466

East Asian (EAS) AF: 0.646 AC: 3337 AN: 5164

South Asian (SAS) AF: 0.470 AC: 2266 AN: 4820

European-Finnish (FIN) AF: 0.474 AC: 4990 AN: 10530

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30549 AN: 67948

Other (OTH) AF: 0.523 AC: 1102 AN: 2108

Alfa AF: 0.477 Hom.: 30075

Bravo AF: 0.574

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.59
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs230271; hg19: chr1-40290597;