rs1474359

Variant names:

• chr2-190068280-T-C
• rs1474359
• ENST00000478197.1:n.220-10943T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-190068280-T-C
• chr2-190068280-T-G

Variant summary

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

The ENST00000478197.1(C2orf88):​n.220-10943T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,110 control chromosomes in the GnomAD database, including 31,666 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 0.60 (31666 hom., cov: 32)
• Consequence: C2orf88 ENST00000478197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 5 publications found

Genes affected

C2orf88 (HGNC:28191): (chromosome 2 open reading frame 88) Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP19	XM_047446008.1	c.-517-11674T>C		intron_variant	Intron 2 of 6		XP_047301964.1
AKAP19	XM_047446009.1	c.-517-11674T>C		intron_variant	Intron 1 of 5		XP_047301965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf88	ENST00000478197.1	n.220-10943T>C		intron_variant	Intron 1 of 1	4
C2orf88	ENST00000495546.1	n.202-11674T>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90697 AN: 151992 Hom.: 31671 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.596 AC: 90694 AN: 152110 Hom.: 31666 Cov.: 32 AF XY: 0.605 AC XY: 44974 AN XY: 74362

African (AFR) AF: 0.201 AC: 8324 AN: 41478

American (AMR) AF: 0.708 AC: 10824 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2170 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3634 AN: 5180

South Asian (SAS) AF: 0.786 AC: 3792 AN: 4826

European-Finnish (FIN) AF: 0.789 AC: 8362 AN: 10592

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51339 AN: 67976

Other (OTH) AF: 0.607 AC: 1275 AN: 2100

Alfa AF: 0.691 Hom.: 73305

Bravo AF: 0.569

Asia WGS AF: 0.694 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.79
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs1474359; hg19: chr2-190933006;