2-202766636-G-A

Variant names:

• chr2-202766636-G-A
• rs11680951
• NM_173511.4:c.*872G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173511.4(FAM117B):​c.*872G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,304 control chromosomes in the GnomAD database, including 18,660 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 0.48 (18616 hom., cov: 30)
  • Exomes 𝑓: 0.44 (44 hom.)
• Consequence: FAM117B NM_173511.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 11 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173511.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM117B	NM_173511.4	MANE Select	c.*872G>A		3_prime_UTR	Exon 8 of 8	NP_775782.2	Q6P1L5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM117B	ENST00000392238.3	TSL:1 MANE Select	c.*872G>A		3_prime_UTR	Exon 8 of 8	ENSP00000376071.2	Q6P1L5-1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73567 AN: 151770 Hom.: 18605 Cov.: 30

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.545

GnomAD4 exome AF: 0.445 AC: 185 AN: 416 Hom.: 44 Cov.: 0 AF XY: 0.464 AC XY: 115 AN XY: 248

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.443 AC: 178 AN: 402

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.625 AC: 5 AN: 8

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.485 AC: 73619 AN: 151888 Hom.: 18616 Cov.: 30 AF XY: 0.479 AC XY: 35547 AN XY: 74240

African (AFR) AF: 0.370 AC: 15305 AN: 41400

American (AMR) AF: 0.487 AC: 7429 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2376 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1487 AN: 5160

South Asian (SAS) AF: 0.529 AC: 2550 AN: 4816

European-Finnish (FIN) AF: 0.407 AC: 4286 AN: 10524

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38130 AN: 67932

Other (OTH) AF: 0.548 AC: 1157 AN: 2112

Alfa AF: 0.540 Hom.: 27740

Bravo AF: 0.482

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.78
PhyloP100		0.024
Mutation Taster		=100/0	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: rs11680951; hg19: chr2-203631359; COSMIC: COSV57419538;