rs934321

Variant names:

• chr10-120954771-A-G
• rs934321
• ENST00000414774.1:n.49+25881T>C

Variant summary

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

The ENST00000414774.1(ENSG00000227307):​n.49+25881T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,152 control chromosomes in the GnomAD database, including 40,176 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 0.73 (40176 hom., cov: 33)
• Consequence: ENSG00000227307 ENST00000414774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 2 publications found

Genes affected

ENSG00000227307 (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 = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378519	XR_001747609.2	n.540+25881T>C		intron_variant	Intron 2 of 2
LOC105378519	XR_946372.3	n.73+25881T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227307	ENST00000414774.1	n.49+25881T>C		intron_variant	Intron 1 of 1	3
ENSG00000310027	ENST00000846644.1	n.59+501A>G		intron_variant	Intron 1 of 1
ENSG00000310027	ENST00000846645.1	n.*67A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110404 AN: 152034 Hom.: 40160 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.726 AC: 110477 AN: 152152 Hom.: 40176 Cov.: 33 AF XY: 0.725 AC XY: 53935 AN XY: 74396

African (AFR) AF: 0.670 AC: 27802 AN: 41490

American (AMR) AF: 0.730 AC: 11157 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2594 AN: 3472

East Asian (EAS) AF: 0.745 AC: 3860 AN: 5180

South Asian (SAS) AF: 0.669 AC: 3227 AN: 4822

European-Finnish (FIN) AF: 0.737 AC: 7806 AN: 10592

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51550 AN: 67998

Other (OTH) AF: 0.705 AC: 1487 AN: 2108

Alfa AF: 0.735 Hom.: 5314

Bravo AF: 0.724

Asia WGS AF: 0.709 AC: 2468 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	1.9
DANN	Benign	0.45
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs934321; hg19: chr10-122714284;