4-69876347-C-T

Position:

• chr4-69876347-C-T

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 0.333 in 151,642 control chromosomes in the GnomAD database, including 8,767 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 0.33 (8767 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50546 AN: 151524 Hom.: 8764 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.333 AC: 50567 AN: 151642 Hom.: 8767 Cov.: 31 AF XY: 0.338 AC XY: 25022 AN XY: 74090

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.362

Alfa AF: 0.316 Hom.: 1404

Bravo AF: 0.324

Asia WGS AF: 0.331 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12506209; hg19: chr4-70742065;