rs1355023

chr6-105805124-T-C

Variant summary

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

The ENST00000644129.1(ENSG00000284999):n.281+24933A>G 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 0.36 in 152,048 control chromosomes in the GnomAD database, including 10,447 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 0.36 (10447 hom., cov: 33)
• Consequence: ENST00000644129.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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
	ENST00000644129.1	n.281+24933A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54642 AN: 151930 Hom.: 10433 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.360 AC: 54703 AN: 152048 Hom.: 10447 Cov.: 33 AF XY: 0.359 AC XY: 26677 AN XY: 74306

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.339

Alfa AF: 0.313 Hom.: 7889

Bravo AF: 0.358

Asia WGS AF: 0.378 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.5
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1355023; hg19: chr6-106252999;