rs1023683

Positions:

• chr15-49415250-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FAM227B	NM_152647.3	c.1013-43851A>T		intron_variant		ENST00000299338.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM227B	ENST00000299338.11	c.1013-43851A>T		intron_variant		2	NM_152647.3	P1

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.203

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023683; hg19: chr15-49707447;