7-145660202-G-C

Variant names:

• chr7-145660202-G-C
• rs4595039
• ENST00000688801.2:n.285+20907C>G

Variant summary

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

The ENST00000688801.2(ENSG00000230746):​n.285+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 ENST00000688801.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

Genes affected

ENSG00000230746 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230746	ENST00000688801.2	n.285+20907C>G		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.729

Alfa AF: 0.639 Hom.: 1729

Bravo AF: 0.741

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4595039; hg19: chr7-145357295;