ENST00000699402.1:c.41-22036A>T

Variant names:

• chr1-161571067-T-A
• rs67418890
• ENST00000699402.1:c.41-22036A>T

Variant summary

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

The ENST00000699402.1(ENSG00000289768):​c.41-22036A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 140,928 control chromosomes in the GnomAD database, including 1,941 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 0.10 (1941 hom., cov: 32)
• Consequence: ENSG00000289768 ENST00000699402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 13 publications found

Genes affected

ENSG00000289768 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000699402.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289768	ENST00000699402.1		c.41-22036A>T		intron	N/A	ENSP00000514363.1
	ENSG00000289768	ENST00000699403.1		c.62-22389A>T		intron	N/A	ENSP00000514364.1
	ENSG00000273112	ENST00000537821.2	TSL:5	n.272-30173T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 14274 AN: 140816 Hom.: 1940 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.0913

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.000818

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.101 AC: 14268 AN: 140928 Hom.: 1941 Cov.: 32 AF XY: 0.101 AC XY: 6928 AN XY: 68772

African (AFR) AF: 0.0267 AC: 957 AN: 35906

American (AMR) AF: 0.110 AC: 1591 AN: 14442

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 680 AN: 3216

East Asian (EAS) AF: 0.000820 AC: 4 AN: 4878

South Asian (SAS) AF: 0.0705 AC: 321 AN: 4556

European-Finnish (FIN) AF: 0.125 AC: 1236 AN: 9918

Middle Eastern (MID) AF: 0.145 AC: 40 AN: 276

European-Non Finnish (NFE) AF: 0.141 AC: 9135 AN: 64958

Other (OTH) AF: 0.117 AC: 228 AN: 1946

Alfa AF: 0.0268 Hom.: 46

Asia WGS AF: 0.0280 AC: 98 AN: 3350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.37
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs67418890; hg19: chr1-161540857;