rs6428058

Variant names:

• chr1-191514531-A-T
• rs6428058

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 152,140 control chromosomes in the GnomAD database, including 4,232 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 (4232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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: 30202 AN: 152022 Hom.: 4211 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.0904

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.199 AC: 30269 AN: 152140 Hom.: 4232 Cov.: 32 AF XY: 0.201 AC XY: 14933 AN XY: 74388

African (AFR) AF: 0.383 AC: 15896 AN: 41474

American (AMR) AF: 0.243 AC: 3709 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 214 AN: 3472

East Asian (EAS) AF: 0.0901 AC: 467 AN: 5186

South Asian (SAS) AF: 0.134 AC: 649 AN: 4828

European-Finnish (FIN) AF: 0.144 AC: 1521 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7247 AN: 68000

Other (OTH) AF: 0.170 AC: 358 AN: 2112

Alfa AF: 0.172 Hom.: 399

Bravo AF: 0.217

Asia WGS AF: 0.125 AC: 436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.39
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs6428058; hg19: chr1-191483661;