rs1360841

Variant names:

• chr6-79172992-T-C
• rs1360841

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.957

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.900

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1360841; hg19: chr6-79882709;