chr4-69264211-C-T

Position:

• chr4-69264211-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 0.145 in 138,898 control chromosomes in the GnomAD database, including 4,178 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 0.15 (4178 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 20163 AN: 138796 Hom.: 4175 Cov.: 30

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.00165

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.145 AC: 20172 AN: 138898 Hom.: 4178 Cov.: 30 AF XY: 0.144 AC XY: 9667 AN XY: 67350

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.00165

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.152

Alfa AF: 0.101 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28625386; hg19: chr4-70129929;