chr2-151290158-G-T

Variant names:

• chr2-151290158-G-T
• rs2278089

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 0.686 in 152,014 control chromosomes in the GnomAD database, including 36,805 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 0.69 (36805 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.686 AC: 104160 AN: 151892 Hom.: 36735 Cov.: 33

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.500 AC: 1 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.686 AC: 104285 AN: 152012 Hom.: 36805 Cov.: 33 AF XY: 0.686 AC XY: 50963 AN XY: 74270

African (AFR) AF: 0.863 AC: 35843 AN: 41530

American (AMR) AF: 0.715 AC: 10920 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1820 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3164 AN: 5162

South Asian (SAS) AF: 0.572 AC: 2756 AN: 4822

European-Finnish (FIN) AF: 0.644 AC: 6770 AN: 10514

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41057 AN: 67930

Other (OTH) AF: 0.632 AC: 1334 AN: 2112

Alfa AF: 0.628 Hom.: 77404

Bravo AF: 0.701

Asia WGS AF: 0.587 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.3
DANN	Benign	0.36
PhyloP100		-0.58
PromoterAI		-0.0090	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2278089; hg19: chr2-152146672;