rs6919798

chr6-32765113-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 0.0593 in 152,222 control chromosomes in the GnomAD database, including 345 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 0.059 (345 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0848 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: 0.0593 AC: 9024 AN: 152104 Hom.: 344 Cov.: 31

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.00622

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0886

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

GnomAD4 genome AF: 0.0593 AC: 9026 AN: 152222 Hom.: 345 Cov.: 31 AF XY: 0.0557 AC XY: 4146 AN XY: 74424

Gnomad4 AFR AF: 0.0672

Gnomad4 AMR AF: 0.0887

Gnomad4 ASJ AF: 0.0525

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.00623

Gnomad4 FIN AF: 0.00528

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0613 Hom.: 151

Bravo AF: 0.0696

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.9
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6919798; hg19: chr6-32732890;