chr5-33985752-T-C

Variant names:

• chr5-33985752-T-C
• rs6867641

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 0.703 in 150,134 control chromosomes in the GnomAD database, including 37,680 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 0.70 (37680 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.703 AC: 105428 AN: 150014 Hom.: 37651 Cov.: 29

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.703 AC: 105502 AN: 150134 Hom.: 37680 Cov.: 29 AF XY: 0.698 AC XY: 51164 AN XY: 73278

African (AFR) AF: 0.818 AC: 33534 AN: 40998

American (AMR) AF: 0.638 AC: 9614 AN: 15078

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2225 AN: 3450

East Asian (EAS) AF: 0.848 AC: 4260 AN: 5026

South Asian (SAS) AF: 0.394 AC: 1841 AN: 4668

European-Finnish (FIN) AF: 0.697 AC: 7154 AN: 10268

Middle Eastern (MID) AF: 0.558 AC: 153 AN: 274

European-Non Finnish (NFE) AF: 0.664 AC: 44737 AN: 67394

Other (OTH) AF: 0.679 AC: 1417 AN: 2088

Alfa AF: 0.681 Hom.: 4314

Bravo AF: 0.715

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.70
DANN	Benign	0.35
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs6867641; hg19: chr5-33985857;