rs11995252

chr8-121609669-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 0.105 in 152,208 control chromosomes in the GnomAD database, including 1,268 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 0.11 (1268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.105 AC: 15988 AN: 152090 Hom.: 1265 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.105 AC: 16010 AN: 152208 Hom.: 1268 Cov.: 32 AF XY: 0.104 AC XY: 7732 AN XY: 74420

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0487

Gnomad4 NFE AF: 0.0665

Gnomad4 OTH AF: 0.0852

Alfa AF: 0.0733 Hom.: 669

Bravo AF: 0.109

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.0
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11995252; hg19: chr8-122621909;