3-69578770-C-G

Variant names:

• chr3-69578770-C-G
• rs736333

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 0.504 in 152,070 control chromosomes in the GnomAD database, including 19,779 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 0.50 (19779 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.597 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: 0.504 AC: 76599 AN: 151952 Hom.: 19768 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.504 AC: 76638 AN: 152070 Hom.: 19779 Cov.: 33 AF XY: 0.506 AC XY: 37614 AN XY: 74336

African (AFR) AF: 0.423 AC: 17533 AN: 41476

American (AMR) AF: 0.607 AC: 9284 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1700 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3027 AN: 5166

South Asian (SAS) AF: 0.545 AC: 2628 AN: 4818

European-Finnish (FIN) AF: 0.486 AC: 5138 AN: 10566

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35776 AN: 67970

Other (OTH) AF: 0.486 AC: 1027 AN: 2114

Alfa AF: 0.527 Hom.: 2631

Bravo AF: 0.508

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs736333; hg19: chr3-69627921;