rs1424558

chr7-136846924-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439694.5(ENSG00000234352):n.344-61033G>C variant causes a intron, non coding transcript 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: ENST00000439694.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586239.5	n.274-61033G>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0192

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.330

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424558; hg19: chr7-136531671;