rs10515199

chr5-74803809-C-T

Variant summary

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

The NM_001376049.1(FAM169A):c.912+684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,144 control chromosomes in the GnomAD database, including 1,874 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 0.15 (1874 hom., cov: 32)
• Consequence: FAM169A NM_001376049.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

Genes affected

FAM169A (HGNC:29138): (family with sequence similarity 169 member A) Predicted to be located in nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM169A	NM_001376049.1	c.912+684G>A		intron_variant		ENST00000687041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM169A	ENST00000687041.1	c.912+684G>A		intron_variant			NM_001376049.1	P1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22224 AN: 152026 Hom.: 1872 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.146 AC: 22241 AN: 152144 Hom.: 1874 Cov.: 32 AF XY: 0.145 AC XY: 10772 AN XY: 74400

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.0993

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.157

Alfa AF: 0.135 Hom.: 198

Bravo AF: 0.152

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.89
Dann	Benign	0.25

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: rs10515199; hg19: chr5-74099634;