5-62778891-G-A

Variant names:

• chr5-62778891-G-A
• rs16891077

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 0.235 in 152,086 control chromosomes in the GnomAD database, including 4,307 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 0.24 (4307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35759 AN: 151968 Hom.: 4311 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.235 AC: 35768 AN: 152086 Hom.: 4307 Cov.: 32 AF XY: 0.236 AC XY: 17526 AN XY: 74340

African (AFR) AF: 0.208 AC: 8643 AN: 41486

American (AMR) AF: 0.232 AC: 3539 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1491 AN: 5164

South Asian (SAS) AF: 0.131 AC: 633 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2619 AN: 10584

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17044 AN: 67980

Other (OTH) AF: 0.250 AC: 527 AN: 2108

Alfa AF: 0.238 Hom.: 8358

Bravo AF: 0.239

Asia WGS AF: 0.183 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.73
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs16891077; hg19: chr5-62074718;