chr2-222809603-G-A

Variant names:

• chr2-222809603-G-A
• rs6436346
• ENST00000764676.1:n.152+9652C>T

Variant summary

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

The ENST00000764676.1(ENSG00000299568):​n.152+9652C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,034 control chromosomes in the GnomAD database, including 38,493 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 0.71 (38493 hom., cov: 31)
• Consequence: ENSG00000299568 ENST00000764676.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 5 publications found

Genes affected

ENSG00000299568 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.812 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
ENSG00000299568	ENST00000764676.1	n.152+9652C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107359 AN: 151916 Hom.: 38442 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.707 AC: 107461 AN: 152034 Hom.: 38493 Cov.: 31 AF XY: 0.702 AC XY: 52151 AN XY: 74310

African (AFR) AF: 0.820 AC: 34021 AN: 41506

American (AMR) AF: 0.620 AC: 9460 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3100 AN: 5170

South Asian (SAS) AF: 0.677 AC: 3266 AN: 4824

European-Finnish (FIN) AF: 0.629 AC: 6627 AN: 10534

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46278 AN: 67974

Other (OTH) AF: 0.693 AC: 1461 AN: 2108

Alfa AF: 0.691 Hom.: 116001

Bravo AF: 0.710

Asia WGS AF: 0.609 AC: 2120 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	1.6
DANN	Benign	0.34
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs6436346; hg19: chr2-223674322;