4-99439570-C-T

Variant names:

• chr4-99439570-C-T
• rs1154476

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 0.313 in 151,992 control chromosomes in the GnomAD database, including 8,243 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 0.31 (8243 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47534 AN: 151874 Hom.: 8238 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.313 AC: 47561 AN: 151992 Hom.: 8243 Cov.: 32 AF XY: 0.316 AC XY: 23494 AN XY: 74270

African (AFR) AF: 0.166 AC: 6877 AN: 41474

American (AMR) AF: 0.395 AC: 6037 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1382 AN: 5160

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4816

European-Finnish (FIN) AF: 0.387 AC: 4078 AN: 10536

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25663 AN: 67950

Other (OTH) AF: 0.308 AC: 649 AN: 2108

Alfa AF: 0.350 Hom.: 32420

Bravo AF: 0.311

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.28
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1154476; hg19: chr4-100360727;