chr15-49412544-G-A

Variant names:

• chr15-49412544-G-A
• rs12591300
• NM_152647.3:c.1013-41145C>T

Variant summary

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

The NM_152647.3(FAM227B):​c.1013-41145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,572 control chromosomes in the GnomAD database, including 6,038 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 0.26 (6038 hom., cov: 31)
• Consequence: FAM227B NM_152647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM227B	NM_152647.3	c.1013-41145C>T		intron_variant	Intron 11 of 15	ENST00000299338.11	NP_689860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM227B	ENST00000299338.11	c.1013-41145C>T		intron_variant	Intron 11 of 15	2	NM_152647.3	ENSP00000299338.6

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38935 AN: 151454 Hom.: 6036 Cov.: 31

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.257 AC: 38918 AN: 151572 Hom.: 6038 Cov.: 31 AF XY: 0.255 AC XY: 18891 AN XY: 74030

African (AFR) AF: 0.0838 AC: 3469 AN: 41374

American (AMR) AF: 0.259 AC: 3939 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3468

East Asian (EAS) AF: 0.187 AC: 960 AN: 5144

South Asian (SAS) AF: 0.211 AC: 1011 AN: 4798

European-Finnish (FIN) AF: 0.307 AC: 3222 AN: 10484

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23955 AN: 67800

Other (OTH) AF: 0.271 AC: 571 AN: 2108

Alfa AF: 0.318 Hom.: 4583

Bravo AF: 0.245

Asia WGS AF: 0.174 AC: 605 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.91
PhyloP100		-0.51
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: rs12591300; hg19: chr15-49704741;