rs165284

Variant names:

• chr1-91057996-A-T
• rs165284

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 0.115 in 152,238 control chromosomes in the GnomAD database, including 1,251 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 0.11 (1251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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: 0.115 AC: 17487 AN: 152120 Hom.: 1252 Cov.: 32

Gnomad AFR AF: 0.0364

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.115 AC: 17482 AN: 152238 Hom.: 1251 Cov.: 32 AF XY: 0.116 AC XY: 8640 AN XY: 74444

African (AFR) AF: 0.0363 AC: 1507 AN: 41558

American (AMR) AF: 0.111 AC: 1700 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3468

East Asian (EAS) AF: 0.0943 AC: 489 AN: 5188

South Asian (SAS) AF: 0.0955 AC: 461 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2127 AN: 10590

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10205 AN: 67998

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.124 Hom.: 153

Bravo AF: 0.107

Asia WGS AF: 0.107 AC: 369 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.2
DANN	Benign	0.77
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs165284; hg19: chr1-91523553;