rs1335546

Variant names:

• chr10-26354604-G-A
• rs1335546
• ENST00000687298.1:n.94-6875C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-26354604-G-A
• chr10-26354604-G-C
• chr10-26354604-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687298.1(ENSG00000289350):​n.94-6875C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,932 control chromosomes in the GnomAD database, including 19,697 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 0.50 (19697 hom., cov: 31)
• Consequence: ENSG00000289350 ENST00000687298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

ENSG00000289350 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 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
ENSG00000289350	ENST00000687298.1	n.94-6875C>T		intron_variant	Intron 1 of 4
ENSG00000289350	ENST00000688112.1	n.100-6870C>T		intron_variant	Intron 1 of 4
ENSG00000289350	ENST00000693700.1	n.82-1556C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76265 AN: 151814 Hom.: 19661 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.503 AC: 76361 AN: 151932 Hom.: 19697 Cov.: 31 AF XY: 0.509 AC XY: 37812 AN XY: 74262

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.494

Alfa AF: 0.491 Hom.: 2627

Bravo AF: 0.503

Asia WGS AF: 0.657 AC: 2285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335546; hg19: chr10-26643533;