rs707341

Positions:

• chr4-2570552-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001366318.2(FAM193A):​c.256-25532C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,194 control chromosomes in the GnomAD database, including 115 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 0.030 (115 hom., cov: 31)
• Consequence: FAM193A NM_001366318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0305 (4639/152194) while in subpopulation NFE AF= 0.0429 (2916/67984). AF 95% confidence interval is 0.0416. There are 115 homozygotes in gnomad4. There are 2324 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 115 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM193A	NM_001366318.2	c.256-25532C>T		intron_variant		ENST00000637812.2	NP_001353247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM193A	ENST00000637812.2	c.256-25532C>T		intron_variant		5	NM_001366318.2	ENSP00000490564	A2

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4642 AN: 152076 Hom.: 115 Cov.: 31

Gnomad AFR AF: 0.00681

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0317

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

GnomAD4 genome AF: 0.0305 AC: 4639 AN: 152194 Hom.: 115 Cov.: 31 AF XY: 0.0312 AC XY: 2324 AN XY: 74402

Gnomad4 AFR AF: 0.00679

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00477

Gnomad4 FIN AF: 0.0703

Gnomad4 NFE AF: 0.0429

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.0378 Hom.: 31

Bravo AF: 0.0257

Asia WGS AF: 0.00375 AC: 13 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	0.40
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs707341; hg19: chr4-2572279;