rs1425658

Variant names:

• chr4-67198813-A-C
• rs1425658
• ENST00000754279.1:n.372+8632T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-67198813-A-C
• chr4-67198813-A-G

Variant summary

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

The ENST00000754279.1(ENSG00000298266):​n.372+8632T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,156 control chromosomes in the GnomAD database, including 47,059 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 0.78 (47059 hom., cov: 32)
• Consequence: ENSG00000298266 ENST00000754279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

Genes affected

ENSG00000298266 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298266	ENST00000754279.1	n.372+8632T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118675 AN: 152038 Hom.: 46990 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.781 AC: 118804 AN: 152156 Hom.: 47059 Cov.: 32 AF XY: 0.782 AC XY: 58157 AN XY: 74362

African (AFR) AF: 0.883 AC: 36675 AN: 41534

American (AMR) AF: 0.820 AC: 12544 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2345 AN: 3468

East Asian (EAS) AF: 0.981 AC: 5081 AN: 5180

South Asian (SAS) AF: 0.900 AC: 4341 AN: 4824

European-Finnish (FIN) AF: 0.679 AC: 7172 AN: 10570

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48143 AN: 67982

Other (OTH) AF: 0.759 AC: 1597 AN: 2104

Alfa AF: 0.728 Hom.: 78761

Bravo AF: 0.793

Asia WGS AF: 0.930 AC: 3228 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	0.95
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1425658; hg19: chr4-68064531;