rs9424490

Variant names:

• chr1-232886124-C-G
• rs9424490
• ENST00000667494.2:n.392-9548C>G

Variant summary

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

The ENST00000667494.2(ENSG00000286774):​n.392-9548C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,938 control chromosomes in the GnomAD database, including 3,219 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 0.15 (3219 hom., cov: 32)
• Consequence: ENSG00000286774 ENST00000667494.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

Genes affected

ENSG00000286774 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927711	XR_247101.4	n.473-9548C>G		intron_variant	Intron 2 of 3
LOC101927711	XR_949278.3	n.963-9548C>G		intron_variant	Intron 4 of 5
LOC101927711	XR_949279.4	n.481-9548C>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286774	ENST00000667494.2	n.392-9548C>G		intron_variant	Intron 2 of 3
ENSG00000286774	ENST00000833157.1	n.377-9548C>G		intron_variant	Intron 2 of 3
ENSG00000286774	ENST00000833158.1	n.377-9548C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22511 AN: 151818 Hom.: 3210 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0911

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.148 AC: 22561 AN: 151938 Hom.: 3219 Cov.: 32 AF XY: 0.146 AC XY: 10820 AN XY: 74266

African (AFR) AF: 0.372 AC: 15412 AN: 41418

American (AMR) AF: 0.146 AC: 2234 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3466

East Asian (EAS) AF: 0.0915 AC: 472 AN: 5160

South Asian (SAS) AF: 0.0478 AC: 230 AN: 4816

European-Finnish (FIN) AF: 0.0601 AC: 635 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0454 AC: 3082 AN: 67928

Other (OTH) AF: 0.124 AC: 262 AN: 2110

Alfa AF: 0.110 Hom.: 246

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9424490; hg19: chr1-233021870;