rs1935193

Variant names:

• chr1-159694300-T-A
• rs1935193
• ENST00000751816.1:n.108-32227T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159694300-T-A
• chr1-159694300-T-C
• chr1-159694300-T-G

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-32227T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,040 control chromosomes in the GnomAD database, including 34,258 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 0.67 (34258 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 7 publications found

Genes affected

ENSG00000297913 (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 (AMR) allele frequency at 95% confidence interval = 0.737 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
ENSG00000297913	ENST00000751816.1	n.108-32227T>A		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-32227T>A		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-32227T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101077 AN: 151922 Hom.: 34237 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.665 AC: 101143 AN: 152040 Hom.: 34258 Cov.: 31 AF XY: 0.667 AC XY: 49547 AN XY: 74310

African (AFR) AF: 0.537 AC: 22252 AN: 41444

American (AMR) AF: 0.749 AC: 11434 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2478 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3396 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2865 AN: 4824

European-Finnish (FIN) AF: 0.749 AC: 7910 AN: 10560

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48455 AN: 67982

Other (OTH) AF: 0.672 AC: 1422 AN: 2116

Alfa AF: 0.690 Hom.: 4522

Bravo AF: 0.662

Asia WGS AF: 0.631 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.32
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1935193; hg19: chr1-159664090;