rs782895

Positions:

• chr7-84901010-A-G
• chr7-84901010-A-T

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 0.279 in 151,950 control chromosomes in the GnomAD database, including 6,217 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 0.28 (6217 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84901010A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42319 AN: 151834 Hom.: 6205 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.279 AC: 42370 AN: 151950 Hom.: 6217 Cov.: 32 AF XY: 0.275 AC XY: 20389 AN XY: 74264

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.272

Alfa AF: 0.254 Hom.: 632

Bravo AF: 0.283

Asia WGS AF: 0.200 AC: 694 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs782895; hg19: chr7-84530326;