11-68148630-C-T

Position:

• chr11-68148630-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 0.518 in 151,848 control chromosomes in the GnomAD database, including 21,521 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 0.52 (21521 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 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: 0.519 AC: 78678 AN: 151730 Hom.: 21511 Cov.: 30

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.518 AC: 78706 AN: 151848 Hom.: 21521 Cov.: 30 AF XY: 0.525 AC XY: 38959 AN XY: 74204

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.559

Alfa AF: 0.379 Hom.: 1107

Bravo AF: 0.520

Asia WGS AF: 0.635 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2512623; hg19: chr11-67916097;