rs6748088

chr2-202691803-T-C

Variant summary

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

The NM_173511.4(FAM117B):c.602-4078T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,028 control chromosomes in the GnomAD database, including 4,579 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 0.22 (4579 hom., cov: 31)
• Consequence: FAM117B NM_173511.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

Genes affected

FAM117B (HGNC:14440): (family with sequence similarity 117 member B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM117B	NM_173511.4	c.602-4078T>C		intron_variant		ENST00000392238.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM117B	ENST00000392238.3	c.602-4078T>C		intron_variant		1	NM_173511.4	P1
FAM117B	ENST00000481658.1	n.301-4078T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34165 AN: 151910 Hom.: 4571 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.225 AC: 34190 AN: 152028 Hom.: 4579 Cov.: 31 AF XY: 0.221 AC XY: 16410 AN XY: 74310

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.276

Alfa AF: 0.255 Hom.: 884

Bravo AF: 0.218

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	7.0
Dann	Benign	0.79

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: rs6748088; hg19: chr2-203556526;