rs12807961

Variant names:

• chr11-34434561-A-G
• rs12807961
• ENST00000724590.1:n.206+1444A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-34434561-A-G
• chr11-34434561-A-T

Variant summary

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

The ENST00000724590.1(ENSG00000294594):​n.206+1444A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,692 control chromosomes in the GnomAD database, including 6,624 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 0.27 (6624 hom., cov: 32)
• Consequence: ENSG00000294594 ENST00000724590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 14 publications found

Genes affected

ENSG00000294594 (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 = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376622	XR_931180.3	n.265+1444A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294594	ENST00000724590.1	n.206+1444A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41533 AN: 151574 Hom.: 6623 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0438

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.274 AC: 41533 AN: 151692 Hom.: 6624 Cov.: 32 AF XY: 0.276 AC XY: 20500 AN XY: 74160

African (AFR) AF: 0.150 AC: 6187 AN: 41268

American (AMR) AF: 0.199 AC: 3043 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 960 AN: 3438

East Asian (EAS) AF: 0.0439 AC: 227 AN: 5176

South Asian (SAS) AF: 0.266 AC: 1280 AN: 4816

European-Finnish (FIN) AF: 0.448 AC: 4734 AN: 10568

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24201 AN: 67864

Other (OTH) AF: 0.237 AC: 497 AN: 2100

Alfa AF: 0.310 Hom.: 9916

Bravo AF: 0.246

Asia WGS AF: 0.146 AC: 509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.39
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12807961; hg19: chr11-34456108;