4-2569969-G-T

Variant names:

• chr4-2569969-G-T
• rs916206
• NM_001366318.2:c.256-26115G>T

Variant summary

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

The NM_001366318.2(FAM193A):​c.256-26115G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,822 control chromosomes in the GnomAD database, including 9,664 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 0.33 (9664 hom., cov: 32)
• Consequence: FAM193A NM_001366318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 1 publications found

Genes affected

FAM193A (HGNC:16822): (family with sequence similarity 193 member A)

ENSG00000290180 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366318.2. 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
	FAM193A	NM_001366318.2	MANE Select	c.256-26115G>T		intron	N/A	NP_001353247.1	A0A1B0GVL4
	FAM193A	NM_001366316.2		c.85-26115G>T		intron	N/A	NP_001353245.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM193A	ENST00000637812.2	TSL:5 MANE Select	c.256-26115G>T		intron	N/A	ENSP00000490564.1	A0A1B0GVL4
	ENSG00000290180	ENST00000703446.1		n.297-26115G>T		intron	N/A	ENSP00000515299.1	H0YAI5
	FAM193A	ENST00000931499.1		c.256-26115G>T		intron	N/A	ENSP00000601558.1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49901 AN: 151706 Hom.: 9653 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.329 AC: 49920 AN: 151822 Hom.: 9664 Cov.: 32 AF XY: 0.334 AC XY: 24758 AN XY: 74196

African (AFR) AF: 0.131 AC: 5406 AN: 41322

American (AMR) AF: 0.527 AC: 8030 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2047 AN: 5176

South Asian (SAS) AF: 0.460 AC: 2215 AN: 4810

European-Finnish (FIN) AF: 0.324 AC: 3420 AN: 10544

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26389 AN: 67938

Other (OTH) AF: 0.328 AC: 694 AN: 2114

Alfa AF: 0.234 Hom.: 738

Bravo AF: 0.337

Asia WGS AF: 0.381 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.58
DANN	Benign	0.69
PhyloP100		-0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs916206; hg19: chr4-2571696;