rs67418890

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-161571067-T-A
• chr1-161571067-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000289768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289768	ENST00000699402.1	c.41-22036A>T		intron_variant	Intron 1 of 3			ENSP00000514363.1
ENSG00000289768	ENST00000699403.1	c.62-22389A>T		intron_variant	Intron 2 of 2			ENSP00000514364.1
ENSG00000273112	ENST00000537821.2	n.272-30173T>A		intron_variant	Intron 3 of 4	5

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

Gnomad4 AFR AF: 0.0267

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.000820

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0268 Hom.: 46

Asia WGS AF: 0.0280 AC: 98 AN: 3350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67418890; hg19: chr1-161540857;