chr1-161980084-C-T

Variant names:

• chr1-161980084-C-T
• rs16834361

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 0.14 in 152,116 control chromosomes in the GnomAD database, including 3,554 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 0.14 (3554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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: 0.140 AC: 21265 AN: 152006 Hom.: 3549 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.00896

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.140 AC: 21290 AN: 152116 Hom.: 3554 Cov.: 32 AF XY: 0.138 AC XY: 10292 AN XY: 74374

African (AFR) AF: 0.406 AC: 16819 AN: 41416

American (AMR) AF: 0.0725 AC: 1109 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3470

East Asian (EAS) AF: 0.0381 AC: 198 AN: 5192

South Asian (SAS) AF: 0.112 AC: 540 AN: 4822

European-Finnish (FIN) AF: 0.00896 AC: 95 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0301 AC: 2045 AN: 68008

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.0770 Hom.: 786

Bravo AF: 0.154

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.57
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs16834361; hg19: chr1-161949874;