rs4599602

Variant names:

• chr6-85448700-C-T
• rs4599602

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 0.239 in 121,940 control chromosomes in the GnomAD database, including 3,377 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 0.24 (3377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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: 0.239 AC: 29126 AN: 121838 Hom.: 3376 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.239 AC: 29152 AN: 121940 Hom.: 3377 Cov.: 32 AF XY: 0.234 AC XY: 13870 AN XY: 59392

African (AFR) AF: 0.351 AC: 13632 AN: 38804

American (AMR) AF: 0.198 AC: 2048 AN: 10352

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 556 AN: 2536

East Asian (EAS) AF: 0.0704 AC: 324 AN: 4602

South Asian (SAS) AF: 0.223 AC: 810 AN: 3628

European-Finnish (FIN) AF: 0.140 AC: 1124 AN: 8012

Middle Eastern (MID) AF: 0.298 AC: 65 AN: 218

European-Non Finnish (NFE) AF: 0.196 AC: 10113 AN: 51566

Other (OTH) AF: 0.221 AC: 357 AN: 1618

Alfa AF: 0.171 Hom.: 326

Bravo AF: 0.198

Asia WGS AF: 0.118 AC: 408 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4599602; hg19: chr6-86158418;