rs1360841

Variant names:

• chr6-79172992-T-C
• rs1360841
• ENST00000759658.1:n.317-28852T>C

Variant summary

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

The ENST00000759658.1(ENSG00000286340):​n.317-28852T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,206 control chromosomes in the GnomAD database, including 59,340 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 0.87 (59340 hom., cov: 32)
• Consequence: ENSG00000286340 ENST00000759658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 1 publications found

Genes affected

ENSG00000286340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000286340	ENST00000759658.1	n.317-28852T>C		intron_variant	Intron 2 of 2
ENSG00000286340	ENST00000759659.1	n.179-7495T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132567 AN: 152088 Hom.: 59326 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.871 AC: 132623 AN: 152206 Hom.: 59340 Cov.: 32 AF XY: 0.874 AC XY: 65062 AN XY: 74416

African (AFR) AF: 0.643 AC: 26658 AN: 41454

American (AMR) AF: 0.921 AC: 14092 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3215 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.984 AC: 4742 AN: 4820

European-Finnish (FIN) AF: 0.957 AC: 10170 AN: 10622

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65524 AN: 68040

Other (OTH) AF: 0.900 AC: 1900 AN: 2112

Alfa AF: 0.905 Hom.: 10000

Bravo AF: 0.857

Asia WGS AF: 0.954 AC: 3315 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.50
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1360841; hg19: chr6-79882709;