chr8-11472035-G-T

Position:

• chr8-11472035-G-T

Variant summary

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

The ENST00000527445.1(FAM167A):​n.107+2574C>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.604

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM167A	XM_011543840.4	c.-398+3831C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM167A	ENST00000527445.1	n.107+2574C>A		intron_variant, non_coding_transcript_variant		1
FAM167A	ENST00000648766.1	c.-398+3831C>A		intron_variant

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

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.346

Alfa AF: 0.313 Hom.: 13346

Bravo AF: 0.332

Asia WGS AF: 0.154 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs899364; hg19: chr8-11329544;