chr1-162065484-T-C

Variant names:

• chr1-162065484-T-C
• rs16847548

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 0.223 in 152,098 control chromosomes in the GnomAD database, including 4,149 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 0.22 (4149 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.55
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 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: 0.223 AC: 33961 AN: 151980 Hom.: 4145 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.223 AC: 33970 AN: 152098 Hom.: 4149 Cov.: 31 AF XY: 0.227 AC XY: 16893 AN XY: 74350

African (AFR) AF: 0.186 AC: 7698 AN: 41496

American (AMR) AF: 0.198 AC: 3028 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1896 AN: 5176

South Asian (SAS) AF: 0.418 AC: 2013 AN: 4820

European-Finnish (FIN) AF: 0.245 AC: 2586 AN: 10556

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15060 AN: 67988

Other (OTH) AF: 0.216 AC: 455 AN: 2106

Alfa AF: 0.221 Hom.: 5914

Bravo AF: 0.214

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.4
DANN	Benign	0.55
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs16847548; hg19: chr1-162035274;