11-1221460-T-C

Variant names:

• chr11-1221460-T-C
• rs868903

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;