rs7760028

Positions:

• chr6-153973938-A-G

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 0.182 in 152,022 control chromosomes in the GnomAD database, including 2,777 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 0.18 (2777 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.153973938A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27635 AN: 151904 Hom.: 2776 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.182 AC: 27633 AN: 152022 Hom.: 2777 Cov.: 32 AF XY: 0.191 AC XY: 14231 AN XY: 74332

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.186

Alfa AF: 0.178 Hom.: 320

Bravo AF: 0.173

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7760028; hg19: chr6-154295073;