rs12160838

chr22-42397557-G-A

Variant summary

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

The NM_145912.8(NFAM1):c.663+301C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,998 control chromosomes in the GnomAD database, including 2,265 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 0.17 (2265 hom., cov: 32)
• Consequence: NFAM1 NM_145912.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

NFAM1 (HGNC:29872): (NFAT activating protein with ITAM motif 1) The protein encoded by this gene is a type I membrane receptor that activates cytokine gene promoters such as the IL-13 and TNF-alpha promoters. The encoded protein contains an immunoreceptor tyrosine-based activation motif (ITAM) and is thought to regulate the signaling and development of B-cells. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFAM1	NM_145912.8	c.663+301C>T		intron_variant		ENST00000329021.10
NFAM1	NM_001318323.3	c.550+301C>T		intron_variant
NFAM1	NM_001371362.1	c.507+301C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFAM1	ENST00000329021.10	c.663+301C>T		intron_variant		1	NM_145912.8	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25312 AN: 151880 Hom.: 2264 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0932

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0890

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.167 AC: 25329 AN: 151998 Hom.: 2265 Cov.: 32 AF XY: 0.165 AC XY: 12271 AN XY: 74284

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0932

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.156

Alfa AF: 0.160 Hom.: 2442

Bravo AF: 0.171

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.090
Dann	Benign	0.47

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: rs12160838; hg19: chr22-42793563;