chr7-145660202-G-C

Position:

• chr7-145660202-G-C

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

Genes affected

(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/exons	MANE	Protein	UniProt
		n.145660202G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230746	ENST00000688801.2	n.285+20907C>G		intron_variant

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;