rs1257010

Positions:

• chr2-96968077-C-A
• chr2-96968077-C-T

Variant summary

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

The NM_001122646.3(FAM178B):​c.627-450G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,426 control chromosomes in the GnomAD database, including 27,446 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 0.53 (27446 hom., cov: 28)
• Consequence: FAM178B NM_001122646.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

FAM178B (HGNC:28036): (family with sequence similarity 178 member B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM178B	NM_001122646.3	c.627-450G>T		intron_variant		ENST00000490605.3	NP_001116118.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM178B	ENST00000490605.3	c.627-450G>T		intron_variant		5	NM_001122646.3	ENSP00000429896	P1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80410 AN: 151308 Hom.: 27453 Cov.: 28

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.531 AC: 80387 AN: 151426 Hom.: 27446 Cov.: 28 AF XY: 0.528 AC XY: 39062 AN XY: 73950

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.540

Alfa AF: 0.621 Hom.: 4071

Bravo AF: 0.491

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1257010; hg19: chr2-97633814;