5-13600505-T-G

Variant names:

• chr5-13600505-T-G
• rs6865300

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 0.575 in 151,962 control chromosomes in the GnomAD database, including 27,167 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 0.57 (27167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.688 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: 0.575 AC: 87286 AN: 151844 Hom.: 27161 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.575 AC: 87323 AN: 151962 Hom.: 27167 Cov.: 32 AF XY: 0.571 AC XY: 42367 AN XY: 74262

African (AFR) AF: 0.377 AC: 15603 AN: 41436

American (AMR) AF: 0.683 AC: 10411 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3468

East Asian (EAS) AF: 0.114 AC: 589 AN: 5164

South Asian (SAS) AF: 0.606 AC: 2918 AN: 4812

European-Finnish (FIN) AF: 0.591 AC: 6236 AN: 10548

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47104 AN: 67976

Other (OTH) AF: 0.604 AC: 1275 AN: 2110

Alfa AF: 0.653 Hom.: 17403

Bravo AF: 0.572

Asia WGS AF: 0.409 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.98
DANN	Benign	0.54
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs6865300; hg19: chr5-13600614;