rs16872345

Variant names:

• chr5-74853653-T-C
• rs16872345
• NM_001376049.1:c.-3-11974A>G

Variant summary

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

The NM_001376049.1(FAM169A):​c.-3-11974A>G 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 151,750 control chromosomes in the GnomAD database, including 1,870 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 (1870 hom., cov: 31)
• Consequence: FAM169A NM_001376049.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 14 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM169A	NM_001376049.1	c.-3-11974A>G		intron_variant	Intron 1 of 12	ENST00000687041.1	NP_001362978.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM169A	ENST00000687041.1	c.-3-11974A>G		intron_variant	Intron 1 of 12		NM_001376049.1	ENSP00000508577.1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22093 AN: 151634 Hom.: 1868 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.146 AC: 22110 AN: 151750 Hom.: 1870 Cov.: 31 AF XY: 0.144 AC XY: 10704 AN XY: 74184

African (AFR) AF: 0.226 AC: 9300 AN: 41232

American (AMR) AF: 0.118 AC: 1798 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3468

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5176

South Asian (SAS) AF: 0.0988 AC: 475 AN: 4810

European-Finnish (FIN) AF: 0.104 AC: 1099 AN: 10532

Middle Eastern (MID) AF: 0.193 AC: 56 AN: 290

European-Non Finnish (NFE) AF: 0.122 AC: 8320 AN: 67986

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.132 Hom.: 5567

Bravo AF: 0.153

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	-0.94
CADD	Benign	0.27
DANN	Benign	0.52
PhyloP100		-1.1
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: rs16872345; hg19: chr5-74149478;