rs6578974

Positions:

• chr11-2074503-C-A
• chr11-2074503-C-G
• chr11-2074503-C-T

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 0.167 in 151,996 control chromosomes in the GnomAD database, including 3,950 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 0.17 (3950 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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: 0.167 AC: 25368 AN: 151878 Hom.: 3937 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.167 AC: 25412 AN: 151996 Hom.: 3950 Cov.: 31 AF XY: 0.161 AC XY: 11952 AN XY: 74312

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.0811

Gnomad4 ASJ AF: 0.0949

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0418

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0792

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0805 Hom.: 1009

Bravo AF: 0.181

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.083
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6578974; hg19: chr11-2095733;