rs16962583

Variant names:

• chr15-49520918-T-C
• rs16962583
• NM_152647.3:c.875-12570A>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.875-12570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,082 control chromosomes in the GnomAD database, including 362 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 0.053 (362 hom., cov: 32)
• Consequence: FAM227B NM_152647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 3 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM227B	NM_152647.3	c.875-12570A>G		intron_variant	Intron 10 of 15	ENST00000299338.11	NP_689860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM227B	ENST00000299338.11	c.875-12570A>G		intron_variant	Intron 10 of 15	2	NM_152647.3	ENSP00000299338.6
FAM227B	ENST00000561064.5	c.773-12570A>G		intron_variant	Intron 9 of 10	1		ENSP00000453028.1

Frequencies

GnomAD3 genomes AF: 0.0527 AC: 8001 AN: 151964 Hom.: 360 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0555

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0527 AC: 8010 AN: 152082 Hom.: 362 Cov.: 32 AF XY: 0.0547 AC XY: 4066 AN XY: 74354

African (AFR) AF: 0.0213 AC: 882 AN: 41500

American (AMR) AF: 0.0684 AC: 1045 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1228 AN: 5144

South Asian (SAS) AF: 0.0767 AC: 369 AN: 4812

European-Finnish (FIN) AF: 0.0428 AC: 453 AN: 10582

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0555 AC: 3771 AN: 67980

Other (OTH) AF: 0.0440 AC: 93 AN: 2114

Alfa AF: 0.0549 Hom.: 325

Bravo AF: 0.0541

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		0.21
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: rs16962583; hg19: chr15-49813115;