rs1321311

Positions:

• chr6-36655123-C-A
• chr6-36655123-C-G

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 0.282 in 152,150 control chromosomes in the GnomAD database, including 6,495 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 0.28 (6495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42871 AN: 152032 Hom.: 6469 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.282 AC: 42943 AN: 152150 Hom.: 6495 Cov.: 32 AF XY: 0.278 AC XY: 20699 AN XY: 74388

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.314

Alfa AF: 0.253 Hom.: 11555

Bravo AF: 0.285

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321311; hg19: chr6-36622900;