rs1424558

Variant names:

• chr7-136846924-C-G
• rs1424558
• ENST00000439694.6:n.656-61033G>C

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.656-61033G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,850 control chromosomes in the GnomAD database, including 9,052 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 0.33 (9052 hom., cov: 31)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 1 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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
ENSG00000234352	ENST00000439694.6	n.656-61033G>C		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000586239.5	n.274-61033G>C		intron_variant	Intron 2 of 4	5
ENSG00000234352	ENST00000592183.5	n.475-61033G>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50542 AN: 151734 Hom.: 9031 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.333 AC: 50603 AN: 151850 Hom.: 9052 Cov.: 31 AF XY: 0.322 AC XY: 23878 AN XY: 74220

African (AFR) AF: 0.404 AC: 16730 AN: 41418

American (AMR) AF: 0.259 AC: 3941 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3470

East Asian (EAS) AF: 0.0192 AC: 99 AN: 5156

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4824

European-Finnish (FIN) AF: 0.244 AC: 2579 AN: 10562

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23880 AN: 67884

Other (OTH) AF: 0.330 AC: 697 AN: 2114

Alfa AF: 0.340 Hom.: 1126

Bravo AF: 0.337

Asia WGS AF: 0.123 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.43
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1424558; hg19: chr7-136531671;