5-34563918-C-T

Variant names:

• chr5-34563918-C-T
• rs6451146

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 0.793 in 152,236 control chromosomes in the GnomAD database, including 48,085 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 0.79 (48085 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.793 AC: 120663 AN: 152118 Hom.: 48060 Cov.: 34

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.793 AC: 120736 AN: 152236 Hom.: 48085 Cov.: 34 AF XY: 0.786 AC XY: 58508 AN XY: 74430

African (AFR) AF: 0.849 AC: 35265 AN: 41544

American (AMR) AF: 0.781 AC: 11955 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2970 AN: 3470

East Asian (EAS) AF: 0.756 AC: 3914 AN: 5176

South Asian (SAS) AF: 0.675 AC: 3257 AN: 4824

European-Finnish (FIN) AF: 0.669 AC: 7095 AN: 10600

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53668 AN: 67998

Other (OTH) AF: 0.787 AC: 1666 AN: 2116

Alfa AF: 0.704 Hom.: 2400

Bravo AF: 0.807

Asia WGS AF: 0.685 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6451146; hg19: chr5-34564023;