3-39755235-G-T

Variant names:

• chr3-39755235-G-T
• rs9878556

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 0.251 in 152,042 control chromosomes in the GnomAD database, including 5,004 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 0.25 (5004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 1 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 = 0.324 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: 0.251 AC: 38176 AN: 151924 Hom.: 4990 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.251 AC: 38217 AN: 152042 Hom.: 5004 Cov.: 32 AF XY: 0.247 AC XY: 18377 AN XY: 74336

African (AFR) AF: 0.329 AC: 13617 AN: 41436

American (AMR) AF: 0.213 AC: 3249 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3468

East Asian (EAS) AF: 0.111 AC: 572 AN: 5176

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2112 AN: 10572

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16072 AN: 67980

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.239 Hom.: 2635

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.71
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs9878556; hg19: chr3-39796726;