6-858970-C-T

Variant names:

• chr6-858970-C-T
• rs1572438

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 0.293 in 152,158 control chromosomes in the GnomAD database, including 6,657 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 0.29 (6657 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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: 0.293 AC: 44512 AN: 152040 Hom.: 6648 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.293 AC: 44537 AN: 152158 Hom.: 6657 Cov.: 33 AF XY: 0.295 AC XY: 21909 AN XY: 74376

African (AFR) AF: 0.265 AC: 10982 AN: 41502

American (AMR) AF: 0.269 AC: 4106 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3468

East Asian (EAS) AF: 0.408 AC: 2112 AN: 5178

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4818

European-Finnish (FIN) AF: 0.281 AC: 2977 AN: 10588

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19956 AN: 68002

Other (OTH) AF: 0.307 AC: 648 AN: 2112

Alfa AF: 0.299 Hom.: 23274

Bravo AF: 0.291

Asia WGS AF: 0.391 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.047
DANN	Benign	0.47
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs1572438; hg19: chr6-858970;