rs2084654

Variant names:

• chr7-129089074-A-G
• rs2084654

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 0.391 in 152,018 control chromosomes in the GnomAD database, including 12,046 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 0.39 (12046 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.391 AC: 59382 AN: 151900 Hom.: 12029 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.391 AC: 59444 AN: 152018 Hom.: 12046 Cov.: 33 AF XY: 0.394 AC XY: 29305 AN XY: 74320

African (AFR) AF: 0.461 AC: 19101 AN: 41462

American (AMR) AF: 0.449 AC: 6856 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3466

East Asian (EAS) AF: 0.463 AC: 2399 AN: 5178

South Asian (SAS) AF: 0.491 AC: 2368 AN: 4826

European-Finnish (FIN) AF: 0.343 AC: 3609 AN: 10530

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22759 AN: 67962

Other (OTH) AF: 0.402 AC: 846 AN: 2106

Alfa AF: 0.358 Hom.: 5541

Bravo AF: 0.396

Asia WGS AF: 0.492 AC: 1709 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.36
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2084654; hg19: chr7-128729128;