rs1324072

chr6-88113218-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 0.138 in 152,206 control chromosomes in the GnomAD database, including 1,555 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 0.14 (1555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 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: 0.138 AC: 21003 AN: 152088 Hom.: 1545 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.138 AC: 21047 AN: 152206 Hom.: 1555 Cov.: 32 AF XY: 0.139 AC XY: 10332 AN XY: 74432

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0498

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.151

Alfa AF: 0.151 Hom.: 212

Bravo AF: 0.132

Asia WGS AF: 0.148 AC: 515 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.9
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324072; hg19: chr6-88822936;