rs11636795

Positions:

• chr15-49383905-T-A
• chr15-49383905-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152647.3(FAM227B):​c.1013-12506A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,926 control chromosomes in the GnomAD database, including 42,406 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 0.74 (42406 hom., cov: 31)
• Consequence: FAM227B NM_152647.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM227B	NM_152647.3	c.1013-12506A>T		intron_variant		ENST00000299338.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM227B	ENST00000299338.11	c.1013-12506A>T		intron_variant		2	NM_152647.3	P1
FAM227B	ENST00000559573.3	n.322+12070A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112928 AN: 151804 Hom.: 42364 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.744 AC: 113030 AN: 151926 Hom.: 42406 Cov.: 31 AF XY: 0.741 AC XY: 55008 AN XY: 74264

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.710

Alfa AF: 0.754 Hom.: 5053

Bravo AF: 0.733

Asia WGS AF: 0.675 AC: 2344 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.66

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: rs11636795; hg19: chr15-49676102;