1-234680808-G-C

Variant names:

• chr1-234680808-G-C
• rs482329
• ENST00000442382.1:n.97-7818C>G

Variant summary

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

The ENST00000449012.2(ENSG00000228044):​n.313-3G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,762 control chromosomes in the GnomAD database, including 26,460 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 0.58 (26404 hom., cov: 28)
  • Exomes 𝑓: 0.61 (56 hom.)
• Consequence: ENSG00000228044 ENST00000449012.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 11 publications found

Genes affected

ENSG00000230628 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449012.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105373209	NR_188651.1		n.123-3G>C		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230628	ENST00000442382.1	TSL:2	n.97-7818C>G		intron	N/A
	ENSG00000228044	ENST00000449012.2	TSL:3	n.313-3G>C		splice_region intron	N/A
	ENSG00000228044	ENST00000453568.1	TSL:5	n.32-3G>C		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87806 AN: 151374 Hom.: 26374 Cov.: 28

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.611 AC: 165 AN: 270 Hom.: 56 Cov.: 0 AF XY: 0.610 AC XY: 100 AN XY: 164

African (AFR) AF: 1.00 AC: 6 AN: 6

American (AMR) AF: 1.00 AC: 4 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AF: 0.750 AC: 6 AN: 8

European-Finnish (FIN) AF: 0.488 AC: 40 AN: 82

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.675 AC: 104 AN: 154

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.580 AC: 87877 AN: 151492 Hom.: 26404 Cov.: 28 AF XY: 0.569 AC XY: 42104 AN XY: 73970

African (AFR) AF: 0.673 AC: 27746 AN: 41256

American (AMR) AF: 0.463 AC: 7056 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1829 AN: 3462

East Asian (EAS) AF: 0.165 AC: 842 AN: 5112

South Asian (SAS) AF: 0.439 AC: 2105 AN: 4796

European-Finnish (FIN) AF: 0.540 AC: 5662 AN: 10478

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.602 AC: 40849 AN: 67832

Other (OTH) AF: 0.565 AC: 1193 AN: 2110

Alfa AF: 0.575 Hom.: 14385

Bravo AF: 0.580

Asia WGS AF: 0.305 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
DANN	Benign	0.64
PhyloP100		0.59

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs482329;

hg19: chr1-234816554;