5-105860727-T-G

Variant names:

• chr5-105860727-T-G
• rs6596651

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 0.596 in 151,918 control chromosomes in the GnomAD database, including 27,168 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 0.60 (27168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 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: 0.597 AC: 90562 AN: 151800 Hom.: 27180 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.596 AC: 90582 AN: 151918 Hom.: 27168 Cov.: 32 AF XY: 0.595 AC XY: 44165 AN XY: 74212

African (AFR) AF: 0.579 AC: 23978 AN: 41440

American (AMR) AF: 0.626 AC: 9561 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2014 AN: 5160

South Asian (SAS) AF: 0.625 AC: 3004 AN: 4808

European-Finnish (FIN) AF: 0.647 AC: 6814 AN: 10538

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41296 AN: 67924

Other (OTH) AF: 0.598 AC: 1261 AN: 2108

Alfa AF: 0.594 Hom.: 20615

Bravo AF: 0.595

Asia WGS AF: 0.485 AC: 1688 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.75
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6596651; hg19: chr5-105196428;