11-1221460-T-C

Position:

• chr11-1221460-T-C

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 0.478 in 152,086 control chromosomes in the GnomAD database, including 17,942 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 0.48 (17942 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

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 = 0.589 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: 0.478 AC: 72694 AN: 151968 Hom.: 17943 Cov.: 34

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.478 AC: 72725 AN: 152086 Hom.: 17942 Cov.: 34 AF XY: 0.480 AC XY: 35675 AN XY: 74340

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.495

Alfa AF: 0.520 Hom.: 14536

Bravo AF: 0.473

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs868903; hg19: chr11-1242690;