10-1899958-C-A

Variant names:

• chr10-1899958-C-A
• rs34167775
• ENST00000733904.1:n.387+1528C>A

Variant summary

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

The ENST00000733904.1(ENSG00000295912):​n.387+1528C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0485 in 152,224 control chromosomes in the GnomAD database, including 241 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 0.049 (241 hom., cov: 32)
• Consequence: ENSG00000295912 ENST00000733904.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 1 publications found

Genes affected

ENSG00000295912 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733904.1. 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
	ENSG00000295912	ENST00000733904.1		n.387+1528C>A		intron	N/A
	ENSG00000295912	ENST00000733905.1		n.368+1528C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0486 AC: 7386 AN: 152106 Hom.: 242 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.0558

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0485 AC: 7389 AN: 152224 Hom.: 241 Cov.: 32 AF XY: 0.0493 AC XY: 3668 AN XY: 74414

African (AFR) AF: 0.0124 AC: 515 AN: 41542

American (AMR) AF: 0.0596 AC: 912 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3472

East Asian (EAS) AF: 0.0432 AC: 224 AN: 5184

South Asian (SAS) AF: 0.0558 AC: 269 AN: 4820

European-Finnish (FIN) AF: 0.0717 AC: 759 AN: 10586

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4342 AN: 68008

Other (OTH) AF: 0.0521 AC: 110 AN: 2110

Alfa AF: 0.0589 Hom.: 26

Bravo AF: 0.0465

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.46
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs34167775; hg19: chr10-1942152;