11-94522093-T-C

Variant names:

• chr11-94522093-T-C
• rs16924603
• NM_001190462.2:c.250+4406T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001190462.2(C11orf97):​c.250+4406T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,150 control chromosomes in the GnomAD database, including 3,186 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 0.19 (3186 hom., cov: 32)
• Consequence: C11orf97 NM_001190462.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 4 publications found

Genes affected

C11orf97 (HGNC:49544): (chromosome 11 open reading frame 97) Predicted to be located in ciliary basal body. Predicted to be active in ciliary base. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001190462.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C11orf97	NM_001190462.2	MANE Select	c.250+4406T>C		intron	N/A	NP_001177391.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C11orf97	ENST00000542198.3	TSL:5 MANE Select	c.250+4406T>C		intron	N/A	ENSP00000490577.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29480 AN: 152032 Hom.: 3185 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.194 AC: 29489 AN: 152150 Hom.: 3186 Cov.: 32 AF XY: 0.196 AC XY: 14588 AN XY: 74366

African (AFR) AF: 0.119 AC: 4926 AN: 41568

American (AMR) AF: 0.144 AC: 2198 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1448 AN: 5178

South Asian (SAS) AF: 0.122 AC: 590 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3284 AN: 10560

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15994 AN: 67954

Other (OTH) AF: 0.170 AC: 359 AN: 2112

Alfa AF: 0.203 Hom.: 572

Bravo AF: 0.180

Asia WGS AF: 0.207 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.55
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs16924603; hg19: chr11-94255259; COSMIC: COSV73377989;