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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414774.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227307	ENST00000414774.1	TSL:3	n.49+25881T>C		intron	N/A
	ENSG00000310027	ENST00000846644.1		n.59+501A>G		intron	N/A
	ENSG00000310027	ENST00000846645.1		n.*67A>G		downstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs934321;

hg19: chr10-122714284;