chr3-152828806-A-G

Variant names:

• chr3-152828806-A-G
• rs1439010

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 0.31 in 152,168 control chromosomes in the GnomAD database, including 11,357 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 0.31 (11357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 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: 0.310 AC: 47067 AN: 152050 Hom.: 11318 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.310 AC: 47161 AN: 152168 Hom.: 11357 Cov.: 32 AF XY: 0.307 AC XY: 22871 AN XY: 74414

African (AFR) AF: 0.676 AC: 28037 AN: 41474

American (AMR) AF: 0.241 AC: 3680 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1388 AN: 5180

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4828

European-Finnish (FIN) AF: 0.143 AC: 1516 AN: 10610

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10117 AN: 68000

Other (OTH) AF: 0.283 AC: 598 AN: 2114

Alfa AF: 0.294 Hom.: 2930

Bravo AF: 0.337

Asia WGS AF: 0.272 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1439010; hg19: chr3-152546595;