rs1470539

Variant names:

• chr7-4463758-C-A
• rs1470539
• ENST00000741164.1:n.175-24239C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-4463758-C-A
• chr7-4463758-C-G

Variant summary

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

The ENST00000741164.1(ENSG00000296681):​n.175-24239C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,196 control chromosomes in the GnomAD database, including 35,218 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 0.67 (35218 hom., cov: 34)
• Consequence: ENSG00000296681 ENST00000741164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 4 publications found

Genes affected

ENSG00000296681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741164.1. 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
	ENSG00000296681	ENST00000741164.1		n.175-24239C>A		intron	N/A
	ENSG00000296681	ENST00000741167.1		n.215-24239C>A		intron	N/A
	ENSG00000296681	ENST00000741168.1		n.255-12402C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102543 AN: 152078 Hom.: 35181 Cov.: 34

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.674 AC: 102630 AN: 152196 Hom.: 35218 Cov.: 34 AF XY: 0.676 AC XY: 50324 AN XY: 74392

African (AFR) AF: 0.804 AC: 33410 AN: 41548

American (AMR) AF: 0.607 AC: 9280 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3472

East Asian (EAS) AF: 0.770 AC: 3992 AN: 5184

South Asian (SAS) AF: 0.622 AC: 3004 AN: 4826

European-Finnish (FIN) AF: 0.683 AC: 7231 AN: 10582

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41643 AN: 67978

Other (OTH) AF: 0.645 AC: 1364 AN: 2116

Alfa AF: 0.605 Hom.: 13160

Bravo AF: 0.673

Asia WGS AF: 0.693 AC: 2410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0060
DANN	Benign	0.76
PhyloP100		-0.82

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1470539;

hg19: chr7-4503389;