5-95450438-C-T

Variant names:

• chr5-95450438-C-T
• rs7709828
• NM_152548.3:c.*156C>T

Variant summary

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

The NM_152548.3(FAM81B):​c.*156C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,265,342 control chromosomes in the GnomAD database, including 20,343 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 0.23 (5491 hom., cov: 32)
  • Exomes 𝑓: 0.15 (14852 hom.)
• Consequence: FAM81B NM_152548.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 5 publications found

Genes affected

FAM81B (HGNC:26335): (family with sequence similarity 81 member B) Located in nucleus. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152548.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM81B	NM_152548.3	MANE Select	c.*156C>T		3_prime_UTR	Exon 10 of 10	NP_689761.2	Q96LP2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM81B	ENST00000283357.10	TSL:1 MANE Select	c.*156C>T		3_prime_UTR	Exon 10 of 10	ENSP00000283357.5	Q96LP2
	FAM81B	ENST00000512365.1	TSL:3	c.*156C>T		3_prime_UTR	Exon 3 of 3	ENSP00000421181.1	H0Y8I8
	FAM81B	ENST00000513110.1	TSL:5	n.*431C>T		non_coding_transcript_exon	Exon 3 of 3	ENSP00000422946.1	H0Y942

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35183 AN: 151704 Hom.: 5471 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.150 AC: 167205 AN: 1113520 Hom.: 14852 Cov.: 14 AF XY: 0.154 AC XY: 85109 AN XY: 554442

African (AFR) AF: 0.456 AC: 10313 AN: 22606

American (AMR) AF: 0.176 AC: 2782 AN: 15776

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 6176 AN: 19690

East Asian (EAS) AF: 0.140 AC: 4188 AN: 29828

South Asian (SAS) AF: 0.242 AC: 14416 AN: 59548

European-Finnish (FIN) AF: 0.107 AC: 4303 AN: 40336

Middle Eastern (MID) AF: 0.319 AC: 1288 AN: 4042

European-Non Finnish (NFE) AF: 0.132 AC: 115620 AN: 875190

Other (OTH) AF: 0.175 AC: 8119 AN: 46504

GnomAD4 genome AF: 0.232 AC: 35231 AN: 151822 Hom.: 5491 Cov.: 32 AF XY: 0.232 AC XY: 17198 AN XY: 74188

African (AFR) AF: 0.441 AC: 18224 AN: 41362

American (AMR) AF: 0.191 AC: 2912 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3466

East Asian (EAS) AF: 0.119 AC: 618 AN: 5182

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4812

European-Finnish (FIN) AF: 0.0975 AC: 1023 AN: 10494

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9609 AN: 67936

Other (OTH) AF: 0.229 AC: 483 AN: 2108

Alfa AF: 0.188 Hom.: 1343

Bravo AF: 0.246

Asia WGS AF: 0.142 AC: 494 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7709828; hg19: chr5-94786142;