rs11694172

Positions:

• chr2-202667581-A-G
• chr2-202667581-A-T

Variant summary

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

The NM_173511.4(FAM117B):​c.602-28300A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,140 control chromosomes in the GnomAD database, including 3,315 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 0.19 (3315 hom., cov: 31)
• Consequence: FAM117B NM_173511.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM117B	NM_173511.4	c.602-28300A>G		intron_variant		ENST00000392238.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM117B	ENST00000392238.3	c.602-28300A>G		intron_variant		1	NM_173511.4	P1
FAM117B	ENST00000481658.1	n.301-28300A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28207 AN: 152022 Hom.: 3325 Cov.: 31

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.185 AC: 28176 AN: 152140 Hom.: 3315 Cov.: 31 AF XY: 0.184 AC XY: 13696 AN XY: 74358

Gnomad4 AFR AF: 0.0537

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.223

Alfa AF: 0.244 Hom.: 7057

Bravo AF: 0.181

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.041
DANN	Benign	0.57

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: rs11694172; hg19: chr2-203532304;