4-71726774-A-T

Variant names:

• chr4-71726774-A-T
• rs16846876

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 0.274 in 152,094 control chromosomes in the GnomAD database, including 6,103 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 0.27 (6103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 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: 0.274 AC: 41664 AN: 151976 Hom.: 6098 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.274 AC: 41688 AN: 152094 Hom.: 6103 Cov.: 32 AF XY: 0.275 AC XY: 20476 AN XY: 74334

African (AFR) AF: 0.178 AC: 7399 AN: 41502

American (AMR) AF: 0.246 AC: 3755 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3464

East Asian (EAS) AF: 0.263 AC: 1361 AN: 5168

South Asian (SAS) AF: 0.285 AC: 1376 AN: 4820

European-Finnish (FIN) AF: 0.352 AC: 3720 AN: 10564

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22177 AN: 67974

Other (OTH) AF: 0.260 AC: 549 AN: 2114

Alfa AF: 0.298 Hom.: 856

Bravo AF: 0.260

Asia WGS AF: 0.265 AC: 925 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.4
DANN	Benign	0.42
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs16846876; hg19: chr4-72592491; COSMIC: COSV66932975;