rs7844834

Positions:

• chr8-11428637-C-A
• chr8-11428637-C-G

Variant summary

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

The NM_053279.3(FAM167A):​c.382-4001G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,108 control chromosomes in the GnomAD database, including 9,919 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 0.34 (9919 hom., cov: 33)
• Consequence: FAM167A NM_053279.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

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

FAM167A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM167A	NM_053279.3	c.382-4001G>T		intron_variant		ENST00000284486.9	NP_444509.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM167A	ENST00000284486.9	c.382-4001G>T		intron_variant		1	NM_053279.3	ENSP00000284486.4

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51377 AN: 151990 Hom.: 9901 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.338 AC: 51435 AN: 152108 Hom.: 9919 Cov.: 33 AF XY: 0.328 AC XY: 24402 AN XY: 74362

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.284

Alfa AF: 0.310 Hom.: 10302

Bravo AF: 0.338

Asia WGS AF: 0.129 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.077
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs7844834; hg19: chr8-11286146;