chr3-78449847-G-T

Variant names:

• chr3-78449847-G-T
• rs9834373

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 0.232 in 151,946 control chromosomes in the GnomAD database, including 5,424 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 0.23 (5424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.929
• Publications: 10 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 (EAS) allele frequency at 95% confidence interval = 0.496 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: 0.232 AC: 35239 AN: 151826 Hom.: 5409 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.232 AC: 35267 AN: 151946 Hom.: 5424 Cov.: 32 AF XY: 0.242 AC XY: 17939 AN XY: 74206

African (AFR) AF: 0.0593 AC: 2462 AN: 41504

American (AMR) AF: 0.370 AC: 5632 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3468

East Asian (EAS) AF: 0.512 AC: 2633 AN: 5144

South Asian (SAS) AF: 0.344 AC: 1659 AN: 4826

European-Finnish (FIN) AF: 0.370 AC: 3889 AN: 10502

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17788 AN: 67954

Other (OTH) AF: 0.206 AC: 435 AN: 2108

Alfa AF: 0.245 Hom.: 4967

Bravo AF: 0.223

Asia WGS AF: 0.367 AC: 1274 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	1.2
DANN	Benign	0.60
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs9834373; hg19: chr3-78498997;