rs11890236

Variant names:

• chr2-104192254-T-C
• rs11890236

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 0.0502 in 152,198 control chromosomes in the GnomAD database, including 199 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 0.050 (199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 4 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 = 0.0732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7634 AN: 152078 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0502 AC: 7644 AN: 152198 Hom.: 199 Cov.: 32 AF XY: 0.0500 AC XY: 3719 AN XY: 74424

African (AFR) AF: 0.0754 AC: 3130 AN: 41536

American (AMR) AF: 0.0518 AC: 791 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3470

East Asian (EAS) AF: 0.0152 AC: 79 AN: 5190

South Asian (SAS) AF: 0.0568 AC: 274 AN: 4822

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0430 AC: 2925 AN: 67968

Other (OTH) AF: 0.0588 AC: 124 AN: 2110

Alfa AF: 0.0470 Hom.: 113

Bravo AF: 0.0520

Asia WGS AF: 0.0760 AC: 264 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs11890236; hg19: chr2-104808712;