8-11472035-G-T

Variant names:

• chr8-11472035-G-T
• rs899364
• ENST00000527445.1:n.107+2574C>A

Variant summary

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

The ENST00000527445.1(FAM167A):​n.107+2574C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,162 control chromosomes in the GnomAD database, including 9,030 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 0.33 (9030 hom., cov: 33)
• Consequence: FAM167A ENST00000527445.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.604
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527445.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM167A	ENST00000527445.1	TSL:1	n.107+2574C>A		intron	N/A
	FAM167A	ENST00000648766.1		c.-398+3831C>A		intron	N/A	ENSP00000497969.1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50088 AN: 152044 Hom.: 9031 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.329 AC: 50095 AN: 152162 Hom.: 9030 Cov.: 33 AF XY: 0.322 AC XY: 23966 AN XY: 74396

African (AFR) AF: 0.441 AC: 18322 AN: 41502

American (AMR) AF: 0.258 AC: 3946 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1157 AN: 3466

East Asian (EAS) AF: 0.0237 AC: 123 AN: 5186

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2690 AN: 10594

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21655 AN: 67996

Other (OTH) AF: 0.346 AC: 730 AN: 2112

Alfa AF: 0.320 Hom.: 31087

Bravo AF: 0.332

Asia WGS AF: 0.154 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.65
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs899364; hg19: chr8-11329544;