5-146409696-T-C

Variant names:

• chr5-146409696-T-C
• rs6868716

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 0.901 in 152,210 control chromosomes in the GnomAD database, including 61,993 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 0.90 (61993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 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: 0.901 AC: 136971 AN: 152092 Hom.: 61931 Cov.: 32

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.901 AC: 137096 AN: 152210 Hom.: 61993 Cov.: 32 AF XY: 0.899 AC XY: 66874 AN XY: 74416

African (AFR) AF: 0.976 AC: 40534 AN: 41542

American (AMR) AF: 0.893 AC: 13656 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3137 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3850 AN: 5166

South Asian (SAS) AF: 0.903 AC: 4360 AN: 4830

European-Finnish (FIN) AF: 0.849 AC: 8986 AN: 10578

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59714 AN: 68010

Other (OTH) AF: 0.898 AC: 1900 AN: 2116

Alfa AF: 0.883 Hom.: 39716

Bravo AF: 0.902

Asia WGS AF: 0.832 AC: 2894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.30
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs6868716; hg19: chr5-145789259;