5-68310056-T-C

Variant names:

• chr5-68310056-T-C
• rs411751

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 0.874 in 152,072 control chromosomes in the GnomAD database, including 58,168 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 0.87 (58168 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.875 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: 0.874 AC: 132871 AN: 151954 Hom.: 58128 Cov.: 29

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.874 AC: 132966 AN: 152072 Hom.: 58168 Cov.: 29 AF XY: 0.873 AC XY: 64848 AN XY: 74322

African (AFR) AF: 0.879 AC: 36467 AN: 41466

American (AMR) AF: 0.854 AC: 13045 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3135 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4543 AN: 5168

South Asian (SAS) AF: 0.790 AC: 3791 AN: 4798

European-Finnish (FIN) AF: 0.865 AC: 9147 AN: 10580

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59881 AN: 67986

Other (OTH) AF: 0.884 AC: 1866 AN: 2112

Alfa AF: 0.883 Hom.: 79622

Bravo AF: 0.877

Asia WGS AF: 0.806 AC: 2805 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	2.1
DANN	Benign	0.74
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs411751; hg19: chr5-67605884;