chr8-11440876-A-G

Variant names:

• chr8-11440876-A-G
• rs9693089
• NM_053279.3:c.381+3155T>C

Variant summary

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

The NM_053279.3(FAM167A):​c.381+3155T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,168 control chromosomes in the GnomAD database, including 35,654 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 0.68 (35654 hom., cov: 33)
• Consequence: FAM167A NM_053279.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM167A	NM_053279.3	c.381+3155T>C		intron_variant	Intron 2 of 2	ENST00000284486.9	NP_444509.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM167A	ENST00000284486.9	c.381+3155T>C		intron_variant	Intron 2 of 2	1	NM_053279.3	ENSP00000284486.4

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103689 AN: 152050 Hom.: 35615 Cov.: 33

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.682 AC: 103793 AN: 152168 Hom.: 35654 Cov.: 33 AF XY: 0.677 AC XY: 50340 AN XY: 74366

African (AFR) AF: 0.774 AC: 32105 AN: 41502

American (AMR) AF: 0.634 AC: 9701 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2115 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3532 AN: 5186

South Asian (SAS) AF: 0.579 AC: 2793 AN: 4826

European-Finnish (FIN) AF: 0.601 AC: 6358 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44907 AN: 67994

Other (OTH) AF: 0.651 AC: 1374 AN: 2112

Alfa AF: 0.683 Hom.: 4436

Bravo AF: 0.694

Asia WGS AF: 0.651 AC: 2262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.62
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9693089; hg19: chr8-11298385;