chr3-78557200-C-T

Variant names:

• chr3-78557200-C-T
• rs10049008

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 0.553 in 151,516 control chromosomes in the GnomAD database, including 23,551 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 0.55 (23551 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.553 AC: 83663 AN: 151396 Hom.: 23530 Cov.: 30

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.553 AC: 83725 AN: 151516 Hom.: 23551 Cov.: 30 AF XY: 0.548 AC XY: 40618 AN XY: 74078

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.570

Alfa AF: 0.543 Hom.: 2466

Bravo AF: 0.562

Asia WGS AF: 0.336 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10049008; hg19: chr3-78606350;