rs6595551

Variant names:

• chr5-124804202-C-T
• rs6595551

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 0.236 in 151,946 control chromosomes in the GnomAD database, including 5,039 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 (5039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.235 AC: 35714 AN: 151828 Hom.: 5013 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.236 AC: 35784 AN: 151946 Hom.: 5039 Cov.: 31 AF XY: 0.235 AC XY: 17420 AN XY: 74256

African (AFR) AF: 0.389 AC: 16127 AN: 41410

American (AMR) AF: 0.140 AC: 2142 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1758 AN: 5156

South Asian (SAS) AF: 0.137 AC: 661 AN: 4830

European-Finnish (FIN) AF: 0.189 AC: 1992 AN: 10540

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11868 AN: 67952

Other (OTH) AF: 0.208 AC: 437 AN: 2106

Alfa AF: 0.194 Hom.: 13985

Bravo AF: 0.241

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.037
DANN	Benign	0.36
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6595551; hg19: chr5-124139895; COSMIC: COSV71946293;