11-103097123-A-C

Position:

• chr11-103097123-A-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 0.045 in 152,262 control chromosomes in the GnomAD database, including 215 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 0.045 (215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0621 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: 0.0450 AC: 6850 AN: 152144 Hom.: 214 Cov.: 32

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.00789

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0450 AC: 6852 AN: 152262 Hom.: 215 Cov.: 32 AF XY: 0.0446 AC XY: 3323 AN XY: 74462

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.0565

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.00791

Gnomad4 SAS AF: 0.0581

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0618 Hom.: 147

Bravo AF: 0.0469

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11225547; hg19: chr11-102967852;