rs1319584

Variant names:

• chr6-142279426-T-C
• rs1319584
• ENST00000849528.1:n.102-10143A>G

Variant summary

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

The ENST00000849528.1(ENSG00000310391):​n.102-10143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,086 control chromosomes in the GnomAD database, including 10,617 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 (10617 hom., cov: 32)
• Consequence: ENSG00000310391 ENST00000849528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 4 publications found

Genes affected

ENSG00000310391 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 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
ENSG00000310391	ENST00000849528.1	n.102-10143A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54403 AN: 151966 Hom.: 10626 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.358 AC: 54407 AN: 152086 Hom.: 10617 Cov.: 32 AF XY: 0.358 AC XY: 26592 AN XY: 74346

African (AFR) AF: 0.202 AC: 8384 AN: 41508

American (AMR) AF: 0.383 AC: 5847 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1569 AN: 3462

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5164

South Asian (SAS) AF: 0.432 AC: 2083 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4341 AN: 10578

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29787 AN: 67962

Other (OTH) AF: 0.375 AC: 790 AN: 2108

Alfa AF: 0.413 Hom.: 51705

Bravo AF: 0.344

Asia WGS AF: 0.332 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.3
DANN	Benign	0.87
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs1319584; hg19: chr6-142600563;