rs3829757

Variant names:

• chr7-22109086-G-A
• rs3829757

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 0.262 in 152,122 control chromosomes in the GnomAD database, including 5,303 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 0.26 (5303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 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: 0.263 AC: 39905 AN: 152004 Hom.: 5295 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.262 AC: 39923 AN: 152122 Hom.: 5303 Cov.: 32 AF XY: 0.261 AC XY: 19413 AN XY: 74362

African (AFR) AF: 0.279 AC: 11573 AN: 41484

American (AMR) AF: 0.304 AC: 4650 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3470

East Asian (EAS) AF: 0.112 AC: 578 AN: 5170

South Asian (SAS) AF: 0.207 AC: 999 AN: 4826

European-Finnish (FIN) AF: 0.231 AC: 2444 AN: 10578

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17821 AN: 67982

Other (OTH) AF: 0.254 AC: 537 AN: 2112

Alfa AF: 0.263 Hom.: 16235

Bravo AF: 0.268

Asia WGS AF: 0.168 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.71
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs3829757; hg19: chr7-22148704;