rs167890

Variant names:

• chr13-110796768-G-A
• rs167890
• ENST00000755406.1:n.439+20031G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-110796768-G-A
• chr13-110796768-G-T

Variant summary

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

The ENST00000755406.1(ENSG00000298419):​n.439+20031G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 152,002 control chromosomes in the GnomAD database, including 451 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 0.074 (451 hom., cov: 30)
• Consequence: ENSG00000298419 ENST00000755406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 4 publications found

Genes affected

ENSG00000298419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755406.1. 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
	ENSG00000298419	ENST00000755406.1		n.439+20031G>A		intron	N/A
	ENSG00000298419	ENST00000755407.1		n.481+19151G>A		intron	N/A
	ENSG00000298419	ENST00000755408.1		n.169+19151G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 11223 AN: 151884 Hom.: 448 Cov.: 30

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0630

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0739 AC: 11239 AN: 152002 Hom.: 451 Cov.: 30 AF XY: 0.0754 AC XY: 5602 AN XY: 74308

African (AFR) AF: 0.0905 AC: 3752 AN: 41444

American (AMR) AF: 0.0551 AC: 842 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.0785 AC: 406 AN: 5172

South Asian (SAS) AF: 0.0627 AC: 302 AN: 4820

European-Finnish (FIN) AF: 0.111 AC: 1168 AN: 10522

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0630 AC: 4283 AN: 67980

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0630 Hom.: 235

Bravo AF: 0.0709

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.33
PhyloP100		-0.75

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: rs167890;

hg19: chr13-111449115;