NM_173511.4:c.602-4078T>C

Variant names:

• chr2-202691803-T-C
• rs6748088
• NM_173511.4:c.602-4078T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM117B	NM_173511.4	c.602-4078T>C		intron_variant	Intron 1 of 7	ENST00000392238.3	NP_775782.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM117B	ENST00000392238.3	c.602-4078T>C		intron_variant	Intron 1 of 7	1	NM_173511.4	ENSP00000376071.2
FAM117B	ENST00000481658.1	n.301-4078T>C		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.105 AC: 4373 AN: 41476

American (AMR) AF: 0.223 AC: 3400 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3472

East Asian (EAS) AF: 0.0581 AC: 301 AN: 5178

South Asian (SAS) AF: 0.132 AC: 636 AN: 4818

European-Finnish (FIN) AF: 0.265 AC: 2798 AN: 10542

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20408 AN: 67954

Other (OTH) AF: 0.276 AC: 581 AN: 2106

Alfa AF: 0.270 Hom.: 1634

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
PhyloP100		0.33
Mutation Taster		=99/1	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: rs6748088; hg19: chr2-203556526;