rs6426870

Variant names:

• chr1-164554716-T-C
• rs6426870

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 0.225 in 152,026 control chromosomes in the GnomAD database, including 5,432 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 0.23 (5432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 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: 0.225 AC: 34225 AN: 151908 Hom.: 5424 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.225 AC: 34245 AN: 152026 Hom.: 5432 Cov.: 32 AF XY: 0.234 AC XY: 17420 AN XY: 74294

African (AFR) AF: 0.0496 AC: 2059 AN: 41496

American (AMR) AF: 0.376 AC: 5740 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3466

East Asian (EAS) AF: 0.699 AC: 3594 AN: 5140

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4816

European-Finnish (FIN) AF: 0.242 AC: 2559 AN: 10558

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16851 AN: 67966

Other (OTH) AF: 0.228 AC: 481 AN: 2112

Alfa AF: 0.262 Hom.: 2215

Bravo AF: 0.229

Asia WGS AF: 0.491 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.6
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs6426870; hg19: chr1-164523953;