rs11856413

Variant names:

• chr15-74907551-A-G
• rs11856413
• ENST00000878718.1:c.-751T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000878718.1(FAM219B):​c.-751T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,122 control chromosomes in the GnomAD database, including 12,245 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 0.35 (12245 hom., cov: 32)
• Consequence: FAM219B ENST00000878718.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 24 publications found

Genes affected

FAM219B (HGNC:24695): (family with sequence similarity 219 member B)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000878718.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM219B	ENST00000878718.1		c.-751T>C		upstream_gene	N/A	ENSP00000548777.1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53630 AN: 152004 Hom.: 12246 Cov.: 32

Gnomad AFR AF: 0.0974

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.353 AC: 53635 AN: 152122 Hom.: 12245 Cov.: 32 AF XY: 0.341 AC XY: 25370 AN XY: 74378

African (AFR) AF: 0.0972 AC: 4036 AN: 41530

American (AMR) AF: 0.409 AC: 6240 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1372 AN: 3470

East Asian (EAS) AF: 0.113 AC: 585 AN: 5180

South Asian (SAS) AF: 0.122 AC: 589 AN: 4822

European-Finnish (FIN) AF: 0.403 AC: 4255 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35351 AN: 67964

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.466 Hom.: 29300

Bravo AF: 0.349

Asia WGS AF: 0.121 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11856413;

hg19: chr15-75199892;