rs10493304

chr1-61201785-T-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001134673.4(NFIA):c.560-75735T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0476 in 152,258 control chromosomes in the GnomAD database, including 264 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 0.048 (264 hom., cov: 32)
• Consequence: NFIA NM_001134673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

NFIA (HGNC:7784): (nuclear factor I A) This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFIA	NM_001134673.4	c.560-75735T>A		intron_variant		ENST00000403491.8
NFIA	NM_001145511.2	c.536-75735T>A		intron_variant
NFIA	NM_001145512.2	c.695-75735T>A		intron_variant
NFIA	NM_005595.5	c.560-75735T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFIA	ENST00000403491.8	c.560-75735T>A		intron_variant		1	NM_001134673.4	P1

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7191 AN: 152140 Hom.: 255 Cov.: 32

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0281

Gnomad FIN AF: 0.0330

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0476 AC: 7240 AN: 152258 Hom.: 264 Cov.: 32 AF XY: 0.0476 AC XY: 3542 AN XY: 74478

Gnomad4 AFR AF: 0.0817

Gnomad4 AMR AF: 0.0312

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.0330

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0392 Hom.: 22

Bravo AF: 0.0506

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	15
Dann	Benign	0.73

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: rs10493304; hg19: chr1-61667457;