rs1900871

Variant names:

• chr2-225146215-C-A
• rs1900871

Your query was ambiguous. Multiple possible variants found:

• chr2-225146215-C-A
• chr2-225146215-C-G
• chr2-225146215-C-T

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 0.987 in 152,240 control chromosomes in the GnomAD database, including 74,205 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 0.99 (74205 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.987 AC: 150103 AN: 152122 Hom.: 74150 Cov.: 31

Gnomad AFR AF: 0.998

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.986

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

GnomAD4 genome AF: 0.987 AC: 150216 AN: 152240 Hom.: 74205 Cov.: 31 AF XY: 0.986 AC XY: 73388 AN XY: 74428

African (AFR) AF: 0.998 AC: 41477 AN: 41570

American (AMR) AF: 0.993 AC: 15187 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3418 AN: 3472

East Asian (EAS) AF: 0.801 AC: 4139 AN: 5168

South Asian (SAS) AF: 0.989 AC: 4776 AN: 4828

European-Finnish (FIN) AF: 0.989 AC: 10484 AN: 10604

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67454 AN: 67990

Other (OTH) AF: 0.985 AC: 2079 AN: 2110

Alfa AF: 0.990 Hom.: 20214

Bravo AF: 0.986

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.40
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1900871; hg19: chr2-226010932;