1-161714831-T-G

Variant names:

• chr1-161714831-T-G
• rs2333749

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 0.658 in 152,018 control chromosomes in the GnomAD database, including 33,078 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 0.66 (33078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99935 AN: 151900 Hom.: 33042 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.658 AC: 100020 AN: 152018 Hom.: 33078 Cov.: 32 AF XY: 0.656 AC XY: 48743 AN XY: 74308

African (AFR) AF: 0.673 AC: 27896 AN: 41450

American (AMR) AF: 0.578 AC: 8829 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2498 AN: 3466

East Asian (EAS) AF: 0.789 AC: 4079 AN: 5170

South Asian (SAS) AF: 0.649 AC: 3134 AN: 4830

European-Finnish (FIN) AF: 0.634 AC: 6687 AN: 10554

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44853 AN: 67956

Other (OTH) AF: 0.671 AC: 1417 AN: 2112

Alfa AF: 0.660 Hom.: 51267

Bravo AF: 0.656

Asia WGS AF: 0.670 AC: 2330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2333749; hg19: chr1-161684621;