5-9978972-T-C

Variant names:

• chr5-9978972-T-C
• rs553169

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 0.679 in 152,146 control chromosomes in the GnomAD database, including 35,308 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 0.68 (35308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 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: 0.679 AC: 103215 AN: 152028 Hom.: 35266 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.679 AC: 103314 AN: 152146 Hom.: 35308 Cov.: 33 AF XY: 0.678 AC XY: 50465 AN XY: 74382

African (AFR) AF: 0.616 AC: 25567 AN: 41508

American (AMR) AF: 0.720 AC: 11007 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2112 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3858 AN: 5170

South Asian (SAS) AF: 0.728 AC: 3508 AN: 4816

European-Finnish (FIN) AF: 0.589 AC: 6242 AN: 10592

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48651 AN: 67990

Other (OTH) AF: 0.683 AC: 1442 AN: 2110

Alfa AF: 0.705 Hom.: 56084

Bravo AF: 0.685

Asia WGS AF: 0.700 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs553169; hg19: chr5-9979084;