chr2-223489965-A-G

Variant names:

• chr2-223489965-A-G
• rs1921650
• ENST00000797088.1:n.189-6321T>C

Variant summary

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

The ENST00000797088.1(ENSG00000303770):​n.189-6321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 152,102 control chromosomes in the GnomAD database, including 835 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 0.068 (835 hom., cov: 32)
• Consequence: ENSG00000303770 ENST00000797088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 2 publications found

Genes affected

ENSG00000303770 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797088.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105373907	NR_187972.1		n.110+788A>G		intron	N/A
	LOC105373907	NR_187973.1		n.110+788A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303770	ENST00000797088.1		n.189-6321T>C		intron	N/A
	ENSG00000303770	ENST00000797089.1		n.43-6321T>C		intron	N/A
	ENSG00000303770	ENST00000797090.1		n.194-9507T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10376 AN: 151984 Hom.: 836 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00474

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0683 AC: 10395 AN: 152102 Hom.: 835 Cov.: 32 AF XY: 0.0707 AC XY: 5260 AN XY: 74352

African (AFR) AF: 0.148 AC: 6147 AN: 41466

American (AMR) AF: 0.112 AC: 1712 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1145 AN: 5162

South Asian (SAS) AF: 0.165 AC: 792 AN: 4814

European-Finnish (FIN) AF: 0.0118 AC: 125 AN: 10600

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00474 AC: 322 AN: 67990

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0393 Hom.: 50

Bravo AF: 0.0820

Asia WGS AF: 0.189 AC: 659 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.79
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1921650; hg19: chr2-224354683;