NM_173611.4:c.532-863C>T

Variant names:

• chr15-38472642-C-T
• rs11073328
• NM_173611.4:c.532-863C>T

Variant summary

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

The NM_173611.4(FAM98B):​c.532-863C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 151,952 control chromosomes in the GnomAD database, including 827 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 0.094 (827 hom., cov: 32)
• Consequence: FAM98B NM_173611.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 19 publications found

Genes affected

FAM98B (HGNC:26773): (family with sequence similarity 98 member B) Enables identical protein binding activity and protein methyltransferase activity. Involved in positive regulation of cell population proliferation; positive regulation of gene expression; and protein methylation. Located in cytoplasm and nucleoplasm. Part of tRNA-splicing ligase complex. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM98B	NM_173611.4	c.532-863C>T		intron_variant	Intron 4 of 7	ENST00000397609.6	NP_775882.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM98B	ENST00000397609.6	c.532-863C>T		intron_variant	Intron 4 of 7	5	NM_173611.4	ENSP00000380734.2
FAM98B	ENST00000491535.5	c.532-863C>T		intron_variant	Intron 4 of 6	1		ENSP00000453166.1
FAM98B	ENST00000559431.1	c.238-863C>T		intron_variant	Intron 2 of 3	5		ENSP00000453926.1

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14312 AN: 151832 Hom.: 824 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0989

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0988

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

GnomAD4 genome AF: 0.0943 AC: 14331 AN: 151952 Hom.: 827 Cov.: 32 AF XY: 0.0962 AC XY: 7138 AN XY: 74238

African (AFR) AF: 0.0316 AC: 1313 AN: 41498

American (AMR) AF: 0.135 AC: 2065 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3462

East Asian (EAS) AF: 0.0991 AC: 513 AN: 5176

South Asian (SAS) AF: 0.155 AC: 744 AN: 4808

European-Finnish (FIN) AF: 0.137 AC: 1441 AN: 10548

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7514 AN: 67896

Other (OTH) AF: 0.104 AC: 219 AN: 2108

Alfa AF: 0.109 Hom.: 4284

Bravo AF: 0.0941

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		0.67
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: rs11073328; hg19: chr15-38764843;