ENST00000434510.2:n.340-2226C>T

Variant names:

• chr22-26165512-G-A
• rs9608466
• ENST00000434510.2:n.340-2226C>T

Variant summary

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

The ENST00000434510.2(ENSG00000229770):​n.340-2226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.09 in 152,258 control chromosomes in the GnomAD database, including 679 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 0.090 (679 hom., cov: 32)
• Consequence: ENSG00000229770 ENST00000434510.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 2 publications found

Genes affected

ENSG00000229770 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372971	NR_188585.1	n.362-992C>T		intron_variant	Intron 2 of 5
LOC105372971	NR_188586.1	n.382-992C>T		intron_variant	Intron 2 of 5
LOC105372971	NR_188587.1	n.261-992C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229770	ENST00000434510.2	n.340-2226C>T		intron_variant	Intron 1 of 3	3
ENSG00000229770	ENST00000650717.1	n.211-992C>T		intron_variant	Intron 2 of 5
ENSG00000229770	ENST00000652418.2	n.235-992C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0897 AC: 13652 AN: 152140 Hom.: 669 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0900 AC: 13697 AN: 152258 Hom.: 679 Cov.: 32 AF XY: 0.0907 AC XY: 6754 AN XY: 74444

African (AFR) AF: 0.109 AC: 4546 AN: 41528

American (AMR) AF: 0.142 AC: 2168 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3470

East Asian (EAS) AF: 0.0780 AC: 405 AN: 5192

South Asian (SAS) AF: 0.106 AC: 510 AN: 4822

European-Finnish (FIN) AF: 0.0611 AC: 649 AN: 10622

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0693 AC: 4714 AN: 68016

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0788 Hom.: 84

Bravo AF: 0.0996

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.17
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs9608466; hg19: chr22-26561478;