rs872411

Variant names:

• chr5-116725686-C-T
• rs872411

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 0.286 in 151,898 control chromosomes in the GnomAD database, including 6,387 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 0.29 (6387 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.286 AC: 43386 AN: 151780 Hom.: 6382 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.286 AC: 43419 AN: 151898 Hom.: 6387 Cov.: 31 AF XY: 0.292 AC XY: 21641 AN XY: 74204

African (AFR) AF: 0.295 AC: 12220 AN: 41408

American (AMR) AF: 0.283 AC: 4319 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3464

East Asian (EAS) AF: 0.446 AC: 2298 AN: 5148

South Asian (SAS) AF: 0.330 AC: 1586 AN: 4808

European-Finnish (FIN) AF: 0.367 AC: 3856 AN: 10520

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17417 AN: 67960

Other (OTH) AF: 0.283 AC: 598 AN: 2112

Alfa AF: 0.266 Hom.: 2135

Bravo AF: 0.279

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.37
DANN	Benign	0.48
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs872411; hg19: chr5-116061382;