chr4-186119310-A-T

Variant names:

• chr4-186119310-A-T
• rs10018625
• NM_001395294.1:c.566+13668A>T

Variant summary

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

The ENST00000706927.1(FAM149A):​c.566+13668A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,224 control chromosomes in the GnomAD database, including 5,297 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 0.25 (5297 hom., cov: 33)
• Consequence: FAM149A ENST00000706927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 5 publications found

Genes affected

FAM149A (HGNC:24527): (family with sequence similarity 149 member A)

LOC124900171 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM149A	NM_001395294.1	MANE Select	c.566+13668A>T		intron	N/A	NP_001382223.1
	FAM149A	NM_001367768.3		c.566+13668A>T		intron	N/A	NP_001354697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM149A	ENST00000706927.1	MANE Select	c.566+13668A>T		intron	N/A	ENSP00000516649.1
	FAM149A	ENST00000850903.1		c.566+13668A>T		intron	N/A	ENSP00000520978.1
	FAM149A	ENST00000389354.7	TSL:5	c.566+13668A>T		intron	N/A	ENSP00000374005.7

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38264 AN: 152106 Hom.: 5295 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.252 AC: 38311 AN: 152224 Hom.: 5297 Cov.: 33 AF XY: 0.245 AC XY: 18210 AN XY: 74448

African (AFR) AF: 0.348 AC: 14463 AN: 41506

American (AMR) AF: 0.184 AC: 2809 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3472

East Asian (EAS) AF: 0.115 AC: 598 AN: 5190

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4818

European-Finnish (FIN) AF: 0.122 AC: 1293 AN: 10612

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15811 AN: 68020

Other (OTH) AF: 0.271 AC: 571 AN: 2106

Alfa AF: 0.247 Hom.: 616

Bravo AF: 0.259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		0.18
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: rs10018625; hg19: chr4-187040464;