rs11664972

Variant names:

• chr18-76095682-T-C
• rs11664972

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 0.401 in 152,072 control chromosomes in the GnomAD database, including 12,798 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 0.40 (12798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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: 0.401 AC: 60954 AN: 151954 Hom.: 12805 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.401 AC: 60942 AN: 152072 Hom.: 12798 Cov.: 32 AF XY: 0.398 AC XY: 29581 AN XY: 74342

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.425

Alfa AF: 0.427 Hom.: 2253

Bravo AF: 0.394

Asia WGS AF: 0.261 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11664972; hg19: chr18-73807637;