5-74863312-C-T

Variant names:

• chr5-74863312-C-T
• rs1993370
• NM_001376049.1:c.-4+2853G>A

Variant summary

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

The NM_001376049.1(FAM169A):​c.-4+2853G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,972 control chromosomes in the GnomAD database, including 7,598 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 0.29 (7598 hom., cov: 33)
• Consequence: FAM169A NM_001376049.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM169A	NM_001376049.1	c.-4+2853G>A		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.-4+2853G>A		intron_variant	Intron 1 of 12		NM_001376049.1	ENSP00000508577.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43724 AN: 151854 Hom.: 7580 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.288 AC: 43784 AN: 151972 Hom.: 7598 Cov.: 33 AF XY: 0.285 AC XY: 21168 AN XY: 74270

African (AFR) AF: 0.487 AC: 20202 AN: 41440

American (AMR) AF: 0.303 AC: 4628 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3468

East Asian (EAS) AF: 0.186 AC: 962 AN: 5164

South Asian (SAS) AF: 0.218 AC: 1048 AN: 4812

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10558

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13722 AN: 67958

Other (OTH) AF: 0.290 AC: 611 AN: 2110

Alfa AF: 0.249 Hom.: 876

Bravo AF: 0.311

Asia WGS AF: 0.240 AC: 835 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.20
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: rs1993370; hg19: chr5-74159137;