rs6894216

Variant names:

• chr5-130456441-C-T
• rs6894216

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 0.419 in 151,520 control chromosomes in the GnomAD database, including 16,364 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 0.42 (16364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 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: 0.419 AC: 63432 AN: 151420 Hom.: 16361 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.419 AC: 63435 AN: 151520 Hom.: 16364 Cov.: 32 AF XY: 0.416 AC XY: 30794 AN XY: 74018

African (AFR) AF: 0.111 AC: 4572 AN: 41334

American (AMR) AF: 0.477 AC: 7253 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1794 AN: 3464

East Asian (EAS) AF: 0.327 AC: 1689 AN: 5166

South Asian (SAS) AF: 0.479 AC: 2305 AN: 4810

European-Finnish (FIN) AF: 0.480 AC: 5024 AN: 10462

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.577 AC: 39109 AN: 67766

Other (OTH) AF: 0.463 AC: 975 AN: 2106

Alfa AF: 0.366 Hom.: 4966

Bravo AF: 0.406

Asia WGS AF: 0.371 AC: 1280 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.1
DANN	Benign	0.79
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs6894216; hg19: chr5-129792134;