chr1-98340865-C-T

Variant names:

• chr1-98340865-C-T
• rs1028889

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 0.299 in 151,942 control chromosomes in the GnomAD database, including 7,225 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 0.30 (7225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45417 AN: 151824 Hom.: 7221 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.299 AC: 45460 AN: 151942 Hom.: 7225 Cov.: 32 AF XY: 0.296 AC XY: 21987 AN XY: 74292

African (AFR) AF: 0.400 AC: 16571 AN: 41420

American (AMR) AF: 0.215 AC: 3279 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1119 AN: 5176

South Asian (SAS) AF: 0.430 AC: 2076 AN: 4828

European-Finnish (FIN) AF: 0.236 AC: 2490 AN: 10556

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18204 AN: 67938

Other (OTH) AF: 0.275 AC: 581 AN: 2110

Alfa AF: 0.278 Hom.: 18557

Bravo AF: 0.295

Asia WGS AF: 0.326 AC: 1130 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1028889; hg19: chr1-98806421;