rs1424574

Variant names:

• chr7-136864286-A-G
• rs1424574
• ENST00000439694.6:n.656-78395T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-136864286-A-G
• chr7-136864286-A-T

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.656-78395T>C variant causes a intron 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: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693
• Publications: 3 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=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439694.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234352	ENST00000439694.6	TSL:1	n.656-78395T>C		intron	N/A
	ENSG00000234352	ENST00000586239.5	TSL:5	n.274-78395T>C		intron	N/A
	ENSG00000234352	ENST00000592183.5	TSL:4	n.475-78395T>C		intron	N/A

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

African (AFR) AF: 0.0787 AC: 3270 AN: 41560

American (AMR) AF: 0.118 AC: 1798 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5172

South Asian (SAS) AF: 0.0785 AC: 379 AN: 4828

European-Finnish (FIN) AF: 0.145 AC: 1533 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11214 AN: 68004

Other (OTH) AF: 0.123 AC: 261 AN: 2116

Alfa AF: 0.149 Hom.: 5683

Bravo AF: 0.121

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	12
DANN	Benign	0.49
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1424574; hg19: chr7-136549033;