rs629448

Variant names:

• chr9-26273324-G-T
• rs629448
• ENST00000844068.1:n.670-11956C>A

Variant summary

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

The ENST00000844068.1(ENSG00000309811):​n.670-11956C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,104 control chromosomes in the GnomAD database, including 4,791 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 0.22 (4791 hom., cov: 33)
• Consequence: ENSG00000309811 ENST00000844068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 4 publications found

Genes affected

ENSG00000309811 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 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
ENSG00000309811	ENST00000844068.1	n.670-11956C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33983 AN: 151986 Hom.: 4791 Cov.: 33

Gnomad AFR AF: 0.0689

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.223 AC: 33989 AN: 152104 Hom.: 4791 Cov.: 33 AF XY: 0.219 AC XY: 16315 AN XY: 74360

African (AFR) AF: 0.0688 AC: 2857 AN: 41528

American (AMR) AF: 0.192 AC: 2927 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3468

East Asian (EAS) AF: 0.0563 AC: 292 AN: 5182

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4826

European-Finnish (FIN) AF: 0.279 AC: 2947 AN: 10554

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22147 AN: 67954

Other (OTH) AF: 0.229 AC: 482 AN: 2108

Alfa AF: 0.295 Hom.: 3318

Bravo AF: 0.206

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.21
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs629448; hg19: chr9-26273322;