rs1424574

Positions:

• chr7-136864286-A-G

Variant summary

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

The ENST00000439694.5(ENSG00000234352):​n.344-78395T>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 0.125 in 152,252 control chromosomes in the GnomAD database, including 1,340 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 0.13 (1340 hom., cov: 32)
• Consequence: ENST00000439694.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000586239.5	n.274-78395T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19063 AN: 152134 Hom.: 1341 Cov.: 32

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.125 AC: 19053 AN: 152252 Hom.: 1340 Cov.: 32 AF XY: 0.122 AC XY: 9065 AN XY: 74426

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0785

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.123

Alfa AF: 0.155 Hom.: 3850

Bravo AF: 0.121

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	12
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424574; hg19: chr7-136549033;