6-93191298-A-G

Variant names:

• chr6-93191298-A-G
• rs1324103

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.35 in 152,020 control chromosomes in the GnomAD database, including 10,551 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 0.35 (10551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.14).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53146 AN: 151902 Hom.: 10546 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.350 AC: 53175 AN: 152020 Hom.: 10551 Cov.: 32 AF XY: 0.353 AC XY: 26253 AN XY: 74290

African (AFR) AF: 0.146 AC: 6062 AN: 41500

American (AMR) AF: 0.435 AC: 6641 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1268 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2272 AN: 5146

South Asian (SAS) AF: 0.357 AC: 1717 AN: 4814

European-Finnish (FIN) AF: 0.439 AC: 4642 AN: 10564

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29318 AN: 67960

Other (OTH) AF: 0.358 AC: 754 AN: 2108

Alfa AF: 0.401 Hom.: 56934

Bravo AF: 0.338

Asia WGS AF: 0.362 AC: 1259 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.14
CADD	Benign	20
DANN	Benign	0.75
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1324103; hg19: chr6-93901016; COSMIC: COSV69413742;