rs11542478

chr2-38938-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001077710.3(FAM110C):c.*2670T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,252 control chromosomes in the GnomAD database, including 1,298 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 0.13 (1298 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: FAM110C NM_001077710.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

FAM110C (HGNC:33340): (family with sequence similarity 110 member C) Enables alpha-tubulin binding activity. Involved in positive regulation of cell migration; positive regulation of protein kinase B signaling; and regulation of cell projection assembly. Located in cell cortex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM110C	NM_001077710.3	c.*2670T>G		3_prime_UTR_variant	2/2	ENST00000327669.5
FAM110C	XM_011510372.3	c.*2696T>G		3_prime_UTR_variant	2/2
FAM110C	XR_001738890.2	n.4084T>G		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM110C	ENST00000327669.5	c.*2670T>G		3_prime_UTR_variant	2/2	1	NM_001077710.3	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19061 AN: 152134 Hom.: 1291 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0735

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.139

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.125 AC: 19089 AN: 152252 Hom.: 1298 Cov.: 33 AF XY: 0.125 AC XY: 9294 AN XY: 74446

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.0647

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.0735

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.145

Alfa AF: 0.134 Hom.: 3104

Bravo AF: 0.133

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.92
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11542478; hg19: chr2-38938;