rs10896449

Variant names:

• chr11-69227200-A-G
• rs10896449
• ENST00000779509.1:n.139-21161A>G

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-21161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,026 control chromosomes in the GnomAD database, including 22,269 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 0.52 (22269 hom., cov: 32)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 122 publications found

Genes affected

ENSG00000301530 (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 (AFR) allele frequency at 95% confidence interval = 0.678 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
ENSG00000301530	ENST00000779509.1	n.139-21161A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79447 AN: 151908 Hom.: 22233 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.523 AC: 79536 AN: 152026 Hom.: 22269 Cov.: 32 AF XY: 0.515 AC XY: 38251 AN XY: 74308

African (AFR) AF: 0.684 AC: 28376 AN: 41470

American (AMR) AF: 0.392 AC: 5983 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3470

East Asian (EAS) AF: 0.0683 AC: 353 AN: 5168

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4945 AN: 10566

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34305 AN: 67946

Other (OTH) AF: 0.536 AC: 1134 AN: 2114

Alfa AF: 0.501 Hom.: 76080

Bravo AF: 0.527

Asia WGS AF: 0.298 AC: 1038 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	3.7
DANN	Benign	0.45
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs10896449; hg19: chr11-68994667;