rs7660462

chr4-186138565-C-T

Variant summary

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

The NM_001395294.1(FAM149A):c.567-10608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,928 control chromosomes in the GnomAD database, including 10,092 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 0.36 (10092 hom., cov: 31)
• Consequence: FAM149A NM_001395294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM149A	NM_001395294.1	c.567-10608C>T		intron_variant		ENST00000706927.1
FAM149A	NM_001367768.3	c.567-10608C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM149A	ENST00000706927.1	c.567-10608C>T		intron_variant			NM_001395294.1	A2
FAM149A	ENST00000389354.7	c.567-10608C>T		intron_variant		5		A2
FAM149A	ENST00000503432.5	c.-307-10608C>T		intron_variant		2		P2
FAM149A	ENST00000508379.5	n.458-10608C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54280 AN: 151810 Hom.: 10081 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.358 AC: 54317 AN: 151928 Hom.: 10092 Cov.: 31 AF XY: 0.353 AC XY: 26204 AN XY: 74248

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.388

Alfa AF: 0.404 Hom.: 26048

Bravo AF: 0.362

Asia WGS AF: 0.334 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.36
Dann	Benign	0.84

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: rs7660462; hg19: chr4-187059719;