8-11475455-G-C

Position:

• chr8-11475455-G-C

Variant summary

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

The ENST00000648766.1(FAM167A):​c.-398+411C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,800 control chromosomes in the GnomAD database, including 8,906 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 0.30 (8906 hom., cov: 31)
• Consequence: FAM167A ENST00000648766.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

FAM167A (HGNC:15549): (family with sequence similarity 167 member A)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM167A	XM_011543840.4	c.-398+411C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM167A	ENST00000648766.1	c.-398+411C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45408 AN: 151682 Hom.: 8887 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.299 AC: 45448 AN: 151800 Hom.: 8906 Cov.: 31 AF XY: 0.308 AC XY: 22858 AN XY: 74180

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.300

Alfa AF: 0.150 Hom.: 276

Bravo AF: 0.309

Asia WGS AF: 0.621 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13257831; hg19: chr8-11332964;