rs10519233

Variant names:

• chr15-49614173-T-C
• rs10519233
• NM_152647.3:c.51+948A>G

Variant summary

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

The NM_152647.3(FAM227B):​c.51+948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,208 control chromosomes in the GnomAD database, including 3,165 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 0.18 (3165 hom., cov: 32)
• Consequence: FAM227B NM_152647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717
• Publications: 4 publications found

Genes affected

FAM227B (HGNC:26543): (family with sequence similarity 227 member B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM227B	NM_152647.3	c.51+948A>G		intron_variant	Intron 2 of 15	ENST00000299338.11	NP_689860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM227B	ENST00000299338.11	c.51+948A>G		intron_variant	Intron 2 of 15	2	NM_152647.3	ENSP00000299338.6

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27992 AN: 152090 Hom.: 3168 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.00461

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.184 AC: 27982 AN: 152208 Hom.: 3165 Cov.: 32 AF XY: 0.186 AC XY: 13831 AN XY: 74420

African (AFR) AF: 0.0629 AC: 2616 AN: 41562

American (AMR) AF: 0.172 AC: 2636 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3472

East Asian (EAS) AF: 0.00481 AC: 25 AN: 5194

South Asian (SAS) AF: 0.174 AC: 842 AN: 4830

European-Finnish (FIN) AF: 0.316 AC: 3338 AN: 10572

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16951 AN: 67982

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.233 Hom.: 4887

Bravo AF: 0.167

Asia WGS AF: 0.0770 AC: 267 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.4
DANN	Benign	0.83
PhyloP100		0.72
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: rs10519233; hg19: chr15-49906370;