rs9616906

Variant names:

• chr22-50666252-G-A
• rs9616906
• ENST00000778025.1:n.40-1275C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-50666252-G-A
• chr22-50666252-G-C

Variant summary

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

The ENST00000778025.1(ENSG00000301328):​n.40-1275C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,972 control chromosomes in the GnomAD database, including 11,498 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 0.38 (11498 hom., cov: 31)
• Consequence: ENSG00000301328 ENST00000778025.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 13 publications found

Genes affected

ENSG00000301328 (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 (NFE) allele frequency at 95% confidence interval = 0.444 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
ENSG00000301328	ENST00000778025.1	n.40-1275C>T		intron_variant	Intron 1 of 1
ENSG00000301328	ENST00000778026.1	n.42-1275C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57029 AN: 151854 Hom.: 11499 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.0717

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.375 AC: 57030 AN: 151972 Hom.: 11498 Cov.: 31 AF XY: 0.368 AC XY: 27362 AN XY: 74268

African (AFR) AF: 0.287 AC: 11902 AN: 41442

American (AMR) AF: 0.321 AC: 4906 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3472

East Asian (EAS) AF: 0.0719 AC: 372 AN: 5176

South Asian (SAS) AF: 0.290 AC: 1398 AN: 4822

European-Finnish (FIN) AF: 0.418 AC: 4409 AN: 10554

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30476 AN: 67936

Other (OTH) AF: 0.408 AC: 860 AN: 2108

Alfa AF: 0.417 Hom.: 36482

Bravo AF: 0.363

Asia WGS AF: 0.195 AC: 678 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	1.8
DANN	Benign	0.49
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs9616906; hg19: chr22-51104680;