rs10018625

Positions:

• chr4-186119310-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395294.1(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 NM_001395294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

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

LOC124900171 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM149A	NM_001395294.1	c.566+13668A>T		intron_variant		ENST00000706927.1
LOC124900171	XR_007058421.1	n.43-3638A>T		intron_variant, non_coding_transcript_variant
FAM149A	NM_001367768.3	c.566+13668A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM149A	ENST00000706927.1	c.566+13668A>T		intron_variant			NM_001395294.1	A2
FAM149A	ENST00000389354.7	c.566+13668A>T		intron_variant		5		A2
FAM149A	ENST00000503432.5	c.-308+14790A>T		intron_variant		2		P2
FAM149A	ENST00000508379.5	n.457+11575A>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.271

Alfa AF: 0.247 Hom.: 616

Bravo AF: 0.259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs10018625; hg19: chr4-187040464;