rs2110728

Variant names:

• chr2-201100955-G-A
• rs2110728

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 0.215 in 151,950 control chromosomes in the GnomAD database, including 4,324 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 0.21 (4324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 15 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 (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.215 AC: 32590 AN: 151832 Hom.: 4316 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00849

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.215 AC: 32634 AN: 151950 Hom.: 4324 Cov.: 32 AF XY: 0.210 AC XY: 15616 AN XY: 74290

African (AFR) AF: 0.366 AC: 15166 AN: 41410

American (AMR) AF: 0.162 AC: 2474 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3466

East Asian (EAS) AF: 0.00851 AC: 44 AN: 5170

South Asian (SAS) AF: 0.0707 AC: 341 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1739 AN: 10574

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11541 AN: 67954

Other (OTH) AF: 0.202 AC: 426 AN: 2104

Alfa AF: 0.177 Hom.: 1476

Bravo AF: 0.223

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.78
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs2110728; hg19: chr2-201965678;