rs1023683

Variant names:

• chr15-49415250-T-A
• rs1023683
• NM_152647.3:c.1013-43851A>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.1013-43851A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,068 control chromosomes in the GnomAD database, including 3,159 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 0.19 (3159 hom., cov: 32)
• Consequence: FAM227B NM_152647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM227B	NM_152647.3	c.1013-43851A>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.1013-43851A>T		intron_variant	Intron 11 of 15	2	NM_152647.3	ENSP00000299338.6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29109 AN: 151950 Hom.: 3158 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.00500

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.192 AC: 29121 AN: 152068 Hom.: 3159 Cov.: 32 AF XY: 0.193 AC XY: 14352 AN XY: 74312

African (AFR) AF: 0.113 AC: 4707 AN: 41526

American (AMR) AF: 0.175 AC: 2665 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3462

East Asian (EAS) AF: 0.00521 AC: 27 AN: 5184

South Asian (SAS) AF: 0.178 AC: 860 AN: 4826

European-Finnish (FIN) AF: 0.286 AC: 3020 AN: 10544

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16253 AN: 67942

Other (OTH) AF: 0.203 AC: 429 AN: 2114

Alfa AF: 0.220 Hom.: 519

Bravo AF: 0.179

Asia WGS AF: 0.0840 AC: 290 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.9
DANN	Benign	0.55
PhyloP100		-0.042
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: rs1023683; hg19: chr15-49707447;