rs1335546

chr10-26354604-G-Achr10-26354604-G-Cchr10-26354604-G-T

Variant summary

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

The ENST00000688112.1(ENSG00000289350):n.100-6870C>T variant causes a intron, non coding transcript 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: ENST00000688112.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000688112.1	n.100-6870C>T		intron_variant, non_coding_transcript_variant
	ENST00000687298.1	n.94-6875C>T		intron_variant, non_coding_transcript_variant
	ENST00000693700.1	n.82-1556C>T		intron_variant, non_coding_transcript_variant

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;