rs11542478

Variant names:

• chr2-38938-A-C
• rs11542478
• NM_001077710.3:c.*2670T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM110C	NM_001077710.3	c.*2670T>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000327669.5	NP_001071178.2
FAM110C	XR_001738890.2	n.4084T>G		non_coding_transcript_exon_variant	Exon 4 of 4
FAM110C	XM_011510372.3	c.*2696T>G		3_prime_UTR_variant	Exon 2 of 2		XP_011508674.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM110C	ENST00000327669.5	c.*2670T>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_001077710.3	ENSP00000328347.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.102 AC: 4252 AN: 41540

American (AMR) AF: 0.192 AC: 2936 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.0647 AC: 336 AN: 5190

South Asian (SAS) AF: 0.214 AC: 1033 AN: 4832

European-Finnish (FIN) AF: 0.0735 AC: 779 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8965 AN: 68008

Other (OTH) AF: 0.145 AC: 307 AN: 2114

Alfa AF: 0.134 Hom.: 4689

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
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11542478; hg19: chr2-38938;