chr5-84968107-T-A

Variant names:

• chr5-84968107-T-A
• rs4704021

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 0.634 in 151,580 control chromosomes in the GnomAD database, including 31,215 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 0.63 (31215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.701 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: 0.634 AC: 96039 AN: 151460 Hom.: 31203 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.683

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.634 AC: 96083 AN: 151580 Hom.: 31215 Cov.: 32 AF XY: 0.631 AC XY: 46735 AN XY: 74052

African (AFR) AF: 0.479 AC: 19836 AN: 41370

American (AMR) AF: 0.712 AC: 10812 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2425 AN: 3466

East Asian (EAS) AF: 0.682 AC: 3514 AN: 5150

South Asian (SAS) AF: 0.603 AC: 2911 AN: 4826

European-Finnish (FIN) AF: 0.637 AC: 6706 AN: 10532

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.702 AC: 47579 AN: 67740

Other (OTH) AF: 0.680 AC: 1435 AN: 2110

Alfa AF: 0.555 Hom.: 1576

Bravo AF: 0.642

Asia WGS AF: 0.613 AC: 2130 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.21
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4704021; hg19: chr5-84263925;