rs1592410

Variant names:

• chr6-29516191-C-T
• rs1592410

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 0.452 in 151,996 control chromosomes in the GnomAD database, including 15,815 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 0.45 (15815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.452 AC: 68630 AN: 151878 Hom.: 15772 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.452 AC: 68714 AN: 151996 Hom.: 15815 Cov.: 32 AF XY: 0.451 AC XY: 33504 AN XY: 74290

African (AFR) AF: 0.509 AC: 21079 AN: 41436

American (AMR) AF: 0.362 AC: 5526 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1451 AN: 5180

South Asian (SAS) AF: 0.517 AC: 2493 AN: 4820

European-Finnish (FIN) AF: 0.519 AC: 5474 AN: 10552

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.445 AC: 30222 AN: 67958

Other (OTH) AF: 0.430 AC: 908 AN: 2110

Alfa AF: 0.443 Hom.: 37017

Bravo AF: 0.439

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.81
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1592410; hg19: chr6-29483968;