3-78557200-C-T

Variant names:

• chr3-78557200-C-T
• rs10049008

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 0.553 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.641 AC: 26450 AN: 41244

American (AMR) AF: 0.530 AC: 8066 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1940 AN: 3462

East Asian (EAS) AF: 0.304 AC: 1562 AN: 5130

South Asian (SAS) AF: 0.381 AC: 1828 AN: 4804

European-Finnish (FIN) AF: 0.533 AC: 5608 AN: 10518

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36330 AN: 67828

Other (OTH) AF: 0.570 AC: 1202 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.85
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10049008; hg19: chr3-78606350;