chr2-121816441-G-A

Variant names:

• chr2-121816441-G-A
• rs10864871

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 0.36 in 152,016 control chromosomes in the GnomAD database, including 10,437 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 0.36 (10437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 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: 0.360 AC: 54684 AN: 151898 Hom.: 10442 Cov.: 33

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.360 AC: 54705 AN: 152016 Hom.: 10437 Cov.: 33 AF XY: 0.365 AC XY: 27133 AN XY: 74318

African (AFR) AF: 0.435 AC: 18034 AN: 41470

American (AMR) AF: 0.399 AC: 6099 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1212 AN: 3470

East Asian (EAS) AF: 0.568 AC: 2920 AN: 5142

South Asian (SAS) AF: 0.289 AC: 1391 AN: 4810

European-Finnish (FIN) AF: 0.372 AC: 3933 AN: 10572

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 20005 AN: 67958

Other (OTH) AF: 0.376 AC: 794 AN: 2114

Alfa AF: 0.316 Hom.: 33664

Bravo AF: 0.368

Asia WGS AF: 0.418 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10864871; hg19: chr2-122574017;