7-84901010-A-G

Variant names:

• chr7-84901010-A-G
• rs782895

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.378 AC: 15668 AN: 41438

American (AMR) AF: 0.240 AC: 3660 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3470

East Asian (EAS) AF: 0.149 AC: 768 AN: 5154

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4812

European-Finnish (FIN) AF: 0.172 AC: 1824 AN: 10574

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17627 AN: 67940

Other (OTH) AF: 0.272 AC: 575 AN: 2112

Alfa AF: 0.259 Hom.: 686

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs782895; hg19: chr7-84530326;