rs1331100

Positions:

• chr6-89168742-A-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 0.359 in 151,840 control chromosomes in the GnomAD database, including 10,697 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 0.36 (10697 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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: 0.358 AC: 54363 AN: 151722 Hom.: 10646 Cov.: 30

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.359 AC: 54477 AN: 151840 Hom.: 10697 Cov.: 30 AF XY: 0.353 AC XY: 26181 AN XY: 74208

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.365

Alfa AF: 0.326 Hom.: 1112

Bravo AF: 0.378

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1331100; hg19: chr6-89878461;