chr4-69902928-T-G

Variant names:

• chr4-69902928-T-G
• rs10518069

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 0.543 in 152,052 control chromosomes in the GnomAD database, including 23,201 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 0.54 (23201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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: 0.543 AC: 82508 AN: 151934 Hom.: 23201 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.543 AC: 82531 AN: 152052 Hom.: 23201 Cov.: 32 AF XY: 0.545 AC XY: 40471 AN XY: 74326

African (AFR) AF: 0.398 AC: 16496 AN: 41472

American (AMR) AF: 0.531 AC: 8108 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2024 AN: 3472

East Asian (EAS) AF: 0.719 AC: 3727 AN: 5180

South Asian (SAS) AF: 0.468 AC: 2259 AN: 4828

European-Finnish (FIN) AF: 0.629 AC: 6645 AN: 10560

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41316 AN: 67960

Other (OTH) AF: 0.564 AC: 1193 AN: 2116

Alfa AF: 0.579 Hom.: 70328

Bravo AF: 0.532

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10518069; hg19: chr4-70768646;