4-69264211-C-T

Variant names:

• chr4-69264211-C-T
• rs28625386

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 0.145 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.102 AC: 3613 AN: 35544

American (AMR) AF: 0.123 AC: 1705 AN: 13868

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 562 AN: 3284

East Asian (EAS) AF: 0.00165 AC: 8 AN: 4844

South Asian (SAS) AF: 0.142 AC: 600 AN: 4224

European-Finnish (FIN) AF: 0.187 AC: 1711 AN: 9162

Middle Eastern (MID) AF: 0.131 AC: 35 AN: 268

European-Non Finnish (NFE) AF: 0.177 AC: 11483 AN: 64934

Other (OTH) AF: 0.152 AC: 291 AN: 1920

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
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs28625386; hg19: chr4-70129929;