rs9608466

chr22-26165512-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434510.2(ENSG00000229770):n.340-2226C>T variant causes a intron, non coding transcript 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: ENST00000434510.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372971	XR_938102.3	n.424-992C>T		intron_variant, non_coding_transcript_variant
LOC105372971	XR_938101.3	n.444-992C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000434510.2	n.340-2226C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000650717.1	n.211-992C>T		intron_variant, non_coding_transcript_variant
	ENST00000652418.1	n.235-992C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0780

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0998

Alfa AF: 0.0785 Hom.: 83

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9608466; hg19: chr22-26561478;