6-93191298-A-G

Variant names:

• chr6-93191298-A-G
• rs1324103

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.350 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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.358

Alfa AF: 0.411 Hom.: 27068

Bravo AF: 0.338

Asia WGS AF: 0.362 AC: 1259 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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