3-38678444-C-T

Variant names:

• chr3-38678444-C-T
• rs9851724

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.729 in 152,056 control chromosomes in the GnomAD database, including 40,938 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 0.73 (40938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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: 0.729 AC: 110692 AN: 151936 Hom.: 40875 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.729 AC: 110814 AN: 152056 Hom.: 40938 Cov.: 32 AF XY: 0.725 AC XY: 53843 AN XY: 74294

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.728

Alfa AF: 0.686 Hom.: 52101

Bravo AF: 0.745

Asia WGS AF: 0.700 AC: 2433 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9851724; hg19: chr3-38719935;