rs11544338

Variant names:

• chr2-202767787-T-C
• rs11544338
• NM_173511.4:c.*2023T>C

Variant summary

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

The NM_173511.4(FAM117B):​c.*2023T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,076 control chromosomes in the GnomAD database, including 18,956 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 0.49 (18956 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: FAM117B NM_173511.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 8 publications found

Genes affected

FAM117B (HGNC:14440): (family with sequence similarity 117 member B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM117B	NM_173511.4	c.*2023T>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000392238.3	NP_775782.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM117B	ENST00000392238.3	c.*2023T>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_173511.4	ENSP00000376071.2

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74430 AN: 151958 Hom.: 18945 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.552

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: 0.490 AC: 74484 AN: 152076 Hom.: 18956 Cov.: 32 AF XY: 0.484 AC XY: 35946 AN XY: 74336

African (AFR) AF: 0.386 AC: 16032 AN: 41494

American (AMR) AF: 0.489 AC: 7466 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2381 AN: 3460

East Asian (EAS) AF: 0.290 AC: 1500 AN: 5178

South Asian (SAS) AF: 0.529 AC: 2547 AN: 4814

European-Finnish (FIN) AF: 0.407 AC: 4305 AN: 10574

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38182 AN: 67972

Other (OTH) AF: 0.554 AC: 1172 AN: 2114

Alfa AF: 0.568 Hom.: 25426

Bravo AF: 0.488

Asia WGS AF: 0.431 AC: 1498 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.46
PhyloP100		0.14
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: rs11544338; hg19: chr2-203632510;