chr5-77984311-T-C

Variant names:

• chr5-77984311-T-C
• rs355412

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 0.693 in 151,994 control chromosomes in the GnomAD database, including 38,341 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 0.69 (38341 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 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: 0.693 AC: 105210 AN: 151876 Hom.: 38273 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.693 AC: 105338 AN: 151994 Hom.: 38341 Cov.: 31 AF XY: 0.694 AC XY: 51574 AN XY: 74262

African (AFR) AF: 0.921 AC: 38202 AN: 41486

American (AMR) AF: 0.562 AC: 8572 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1942 AN: 3466

East Asian (EAS) AF: 0.923 AC: 4759 AN: 5156

South Asian (SAS) AF: 0.725 AC: 3492 AN: 4818

European-Finnish (FIN) AF: 0.643 AC: 6778 AN: 10540

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39432 AN: 67960

Other (OTH) AF: 0.680 AC: 1430 AN: 2104

Alfa AF: 0.605 Hom.: 45791

Bravo AF: 0.698

Asia WGS AF: 0.831 AC: 2890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.40
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs355412; hg19: chr5-77280135;