rs1322846

Variant names:

• chr6-17240923-T-C
• rs1322846
• ENST00000659730.1:n.236-13373A>G

Variant summary

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

The ENST00000659730.1(ENSG00000287559):​n.236-13373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,030 control chromosomes in the GnomAD database, including 11,821 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 0.39 (11821 hom., cov: 32)
• Consequence: ENSG00000287559 ENST00000659730.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

ENSG00000287559 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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
ENSG00000287559	ENST00000659730.1	n.236-13373A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59243 AN: 151910 Hom.: 11815 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.390 AC: 59272 AN: 152030 Hom.: 11821 Cov.: 32 AF XY: 0.391 AC XY: 29036 AN XY: 74316

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.390

Alfa AF: 0.423 Hom.: 18778

Bravo AF: 0.375

Asia WGS AF: 0.341 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322846; hg19: chr6-17241154;