rs2166219

Variant names:

• chr2-19417541-T-C
• rs2166219
• ENST00000811606.1:n.178-18349A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000811606.1(ENSG00000305536):​n.178-18349A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,878 control chromosomes in the GnomAD database, including 13,662 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 0.41 (13662 hom., cov: 32)
• Consequence: ENSG00000305536 ENST00000811606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 5 publications found

Genes affected

ENSG00000305536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 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
ENSG00000305536	ENST00000811606.1	n.178-18349A>G		intron_variant	Intron 1 of 2
ENSG00000305536	ENST00000811607.1	n.178-18349A>G		intron_variant	Intron 1 of 2
ENSG00000305536	ENST00000811608.1	n.41-11474A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62486 AN: 151760 Hom.: 13630 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.412 AC: 62575 AN: 151878 Hom.: 13662 Cov.: 32 AF XY: 0.419 AC XY: 31057 AN XY: 74192

African (AFR) AF: 0.425 AC: 17609 AN: 41386

American (AMR) AF: 0.549 AC: 8375 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1170 AN: 3470

East Asian (EAS) AF: 0.787 AC: 4065 AN: 5162

South Asian (SAS) AF: 0.441 AC: 2122 AN: 4808

European-Finnish (FIN) AF: 0.382 AC: 4023 AN: 10542

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24019 AN: 67930

Other (OTH) AF: 0.435 AC: 917 AN: 2110

Alfa AF: 0.380 Hom.: 35365

Bravo AF: 0.427

Asia WGS AF: 0.618 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.052
DANN	Benign	0.56
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2166219; hg19: chr2-19617302;