rs1708558

Variant names:

• chr6-66339513-T-C
• rs1708558

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 0.199 in 152,154 control chromosomes in the GnomAD database, including 3,506 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 0.20 (3506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.199 AC: 30218 AN: 152036 Hom.: 3502 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.199 AC: 30238 AN: 152154 Hom.: 3506 Cov.: 33 AF XY: 0.196 AC XY: 14556 AN XY: 74390

African (AFR) AF: 0.297 AC: 12335 AN: 41506

American (AMR) AF: 0.203 AC: 3108 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2097 AN: 5152

South Asian (SAS) AF: 0.179 AC: 866 AN: 4826

European-Finnish (FIN) AF: 0.0515 AC: 547 AN: 10618

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9763 AN: 67994

Other (OTH) AF: 0.219 AC: 461 AN: 2108

Alfa AF: 0.167 Hom.: 3741

Bravo AF: 0.217

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.7
DANN	Benign	0.69
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1708558; hg19: chr6-67049406;