rs1321312

Positions:

• chr6-36655097-C-G
• chr6-36655097-C-T

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 0.916 in 152,292 control chromosomes in the GnomAD database, including 64,100 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 0.92 (64100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.744

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 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

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139375 AN: 152174 Hom.: 64038 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.916 AC: 139496 AN: 152292 Hom.: 64100 Cov.: 32 AF XY: 0.913 AC XY: 67968 AN XY: 74448

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.899

Alfa AF: 0.905 Hom.: 7760

Bravo AF: 0.920

Asia WGS AF: 0.931 AC: 3239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321312; hg19: chr6-36622874;