7-145660202-G-C

Variant names:

• chr7-145660202-G-C
• rs4595039
• ENST00000688801.3:n.452+20907C>G

Variant summary

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

The ENST00000688801.3(ENSG00000230746):​n.452+20907C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,904 control chromosomes in the GnomAD database, including 41,653 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 0.74 (41653 hom., cov: 30)
• Consequence: ENSG00000230746 ENST00000688801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 1 publications found

Genes affected

ENSG00000230746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688801.3. 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
	ENSG00000230746	ENST00000688801.3		n.452+20907C>G		intron	N/A
	ENSG00000230746	ENST00000839561.1		n.286-11806C>G		intron	N/A
	ENSG00000230746	ENST00000839562.1		n.398-11806C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111923 AN: 151786 Hom.: 41621 Cov.: 30

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.737 AC: 112010 AN: 151904 Hom.: 41653 Cov.: 30 AF XY: 0.733 AC XY: 54388 AN XY: 74234

African (AFR) AF: 0.845 AC: 35007 AN: 41452

American (AMR) AF: 0.672 AC: 10255 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2468 AN: 3460

East Asian (EAS) AF: 0.573 AC: 2937 AN: 5126

South Asian (SAS) AF: 0.616 AC: 2962 AN: 4806

European-Finnish (FIN) AF: 0.707 AC: 7460 AN: 10546

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48450 AN: 67946

Other (OTH) AF: 0.729 AC: 1539 AN: 2110

Alfa AF: 0.639 Hom.: 1729

Bravo AF: 0.741

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.27
PhyloP100		-2.9

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: rs4595039;

hg19: chr7-145357295;