rs1993370

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-74863312-C-A
• chr5-74863312-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001376049.1(FAM169A):​c.-4+2853G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376049.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM169A	NM_001376049.1	MANE Select	c.-4+2853G>T		intron	N/A	NP_001362978.1	Q9Y6X4-1
	FAM169A	NM_001376050.1		c.-4+2018G>T		intron	N/A	NP_001362979.1	Q9Y6X4-1
	FAM169A	NM_001376051.1		c.-4+2030G>T		intron	N/A	NP_001362980.1	Q9Y6X4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM169A	ENST00000687041.1	MANE Select	c.-4+2853G>T		intron	N/A	ENSP00000508577.1	Q9Y6X4-1
	FAM169A	ENST00000389156.9	TSL:1	c.-4+3439G>T		intron	N/A	ENSP00000373808.4	Q9Y6X4-1
	FAM169A	ENST00000510609.5	TSL:1	n.-4+2853G>T		intron	N/A	ENSP00000423905.1	Q9Y6X4-2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 876

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.10
DANN	Benign	0.26
PhyloP100		-1.1

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;