rs11623866

Variant names:

• chr14-64986345-G-C
• rs11623866
• ENST00000549987.1:c.247-17904G>C

Variant summary

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

The ENST00000549987.1(CHURC1-FNTB):​c.247-17904G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,014 control chromosomes in the GnomAD database, including 11,615 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 0.39 (11615 hom., cov: 32)
• Consequence: CHURC1-FNTB ENST00000549987.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 9 publications found

Genes affected

CHURC1-FNTB (HGNC:42960): (CHURC1-FNTB readthrough) This locus represents naturally occurring read-through transcription between the neighboring CHURC1 (churchill domain containing 1) and FNTB (farnesyltransferase, CAAX box, beta) on chromosome 14. The read-through transcript produces a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Feb 2011]

LOC107984655 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984655	XR_001750792.2	n.689C>G		non_coding_transcript_exon_variant	Exon 2 of 2
CHURC1-FNTB	NM_001202559.1	c.328-17904G>C		intron_variant	Intron 3 of 13		NP_001189488.1
CHURC1-FNTB	NM_001202558.2	c.7-17904G>C		intron_variant	Intron 2 of 12		NP_001189487.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHURC1-FNTB	ENST00000549987.1	c.247-17904G>C		intron_variant	Intron 3 of 13	2		ENSP00000447121.2

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58858 AN: 151894 Hom.: 11597 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.388 AC: 58932 AN: 152014 Hom.: 11615 Cov.: 32 AF XY: 0.388 AC XY: 28787 AN XY: 74288

African (AFR) AF: 0.366 AC: 15154 AN: 41428

American (AMR) AF: 0.407 AC: 6218 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3472

East Asian (EAS) AF: 0.437 AC: 2256 AN: 5166

South Asian (SAS) AF: 0.313 AC: 1511 AN: 4828

European-Finnish (FIN) AF: 0.412 AC: 4353 AN: 10558

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26697 AN: 67966

Other (OTH) AF: 0.382 AC: 805 AN: 2106

Alfa AF: 0.387 Hom.: 1482

Bravo AF: 0.394

Asia WGS AF: 0.400 AC: 1393 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	2.3
DANN	Benign	0.54
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11623866; hg19: chr14-65453063;