rs6812193

chr4-76277833-C-T

Variant summary

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

The NM_001136570.3(FAM47E):c.871-236C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,046 control chromosomes in the GnomAD database, including 11,039 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 0.37 (11039 hom., cov: 32)
• Consequence: FAM47E NM_001136570.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

FAM47E (HGNC:34343): (family with sequence similarity 47 member E) Enables enzyme activator activity. Involved in positive regulation of histone methylation and protein localization to chromatin. Located in chromatin; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FAM47E-STBD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM47E	NM_001136570.3	c.871-236C>T		intron_variant		ENST00000424749.7
FAM47E-STBD1	NM_001242939.2	c.871-236C>T		intron_variant
FAM47E	NM_001242936.1	c.577-236C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM47E	ENST00000424749.7	c.871-236C>T		intron_variant		5	NM_001136570.3	P1
	ENST00000670253.1	n.278-15581G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56711 AN: 151926 Hom.: 11034 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.373 AC: 56762 AN: 152046 Hom.: 11039 Cov.: 32 AF XY: 0.370 AC XY: 27475 AN XY: 74326

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0823

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.370

Alfa AF: 0.360 Hom.: 22519

Bravo AF: 0.368

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.5
Dann	Benign	0.61

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: rs6812193; hg19: chr4-77198986;