11-67265605-C-T

Position:

• chr11-67265605-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0264 in 152,204 control chromosomes in the GnomAD database, including 80 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 0.026 (80 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0264 (4013/152204) while in subpopulation NFE AF= 0.0438 (2981/67982). AF 95% confidence interval is 0.0425. There are 80 homozygotes in gnomad4. There are 1817 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 80 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67265605C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4017 AN: 152086 Hom.: 80 Cov.: 31

Gnomad AFR AF: 0.00703

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0264 AC: 4013 AN: 152204 Hom.: 80 Cov.: 31 AF XY: 0.0244 AC XY: 1817 AN XY: 74414

Gnomad4 AFR AF: 0.00701

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0102

Gnomad4 FIN AF: 0.0134

Gnomad4 NFE AF: 0.0438

Gnomad4 OTH AF: 0.0299

Alfa AF: 0.0410 Hom.: 161

Bravo AF: 0.0270

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11605263; hg19: chr11-67033076;