4-2569969-G-T

Position:

• chr4-2569969-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM193A	NM_001366318.2	c.256-26115G>T		intron_variant		ENST00000637812.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM193A	ENST00000637812.2	c.256-26115G>T		intron_variant		5	NM_001366318.2	A2

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.328

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916206; hg19: chr4-2571696;