rs11636795

Variant names:

• chr15-49383905-T-A
• rs11636795
• NM_152647.3:c.1013-12506A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_152647.3(FAM227B):​c.1013-12506A>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
• Publications: 0 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=-0.94).
• 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 rank	MANE	Protein	UniProt
FAM227B	NM_152647.3	c.1013-12506A>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.1013-12506A>T		intron_variant	Intron 11 of 15	2	NM_152647.3	ENSP00000299338.6
FAM227B	ENST00000559573.3	n.322+12070A>T		intron_variant	Intron 2 of 4	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

African (AFR) AF: 0.790 AC: 32774 AN: 41466

American (AMR) AF: 0.636 AC: 9669 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2725 AN: 3462

East Asian (EAS) AF: 0.556 AC: 2873 AN: 5166

South Asian (SAS) AF: 0.737 AC: 3548 AN: 4814

European-Finnish (FIN) AF: 0.755 AC: 7984 AN: 10576

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51016 AN: 67910

Other (OTH) AF: 0.710 AC: 1500 AN: 2112

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
PhyloP100		-0.19
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: rs11636795; hg19: chr15-49676102;