rs1331100

Variant names:

• chr6-89168742-A-G
• rs1331100

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.526 AC: 21787 AN: 41386

American (AMR) AF: 0.364 AC: 5548 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1322 AN: 5160

South Asian (SAS) AF: 0.240 AC: 1153 AN: 4814

European-Finnish (FIN) AF: 0.284 AC: 2984 AN: 10514

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19438 AN: 67926

Other (OTH) AF: 0.365 AC: 770 AN: 2110

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
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1331100; hg19: chr6-89878461;