chr1-61077852-C-CT

Position:

• chr1-61077852-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000371191.5(NFIA):​c.97-10283dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 113,374 control chromosomes in the GnomAD database, including 67 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.024 (67 hom., cov: 31)
• Consequence: NFIA ENST00000371191.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.959

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.

• BP6: Variant 1-61077852-C-CT is Benign according to our data. Variant chr1-61077852-C-CT is described in ClinVar as [Benign]. Clinvar id is 1231072.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFIA	NM_001145511.2	c.3+238dup		intron_variant			NP_001138983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFIA	ENST00000371191.5	c.97-10283dup		intron_variant		5		ENSP00000360233
NFIA	ENST00000407417.7	c.3+238dup		intron_variant		2		ENSP00000384680
NFIA	ENST00000476646.5	c.-114-10283dup		intron_variant		3		ENSP00000474461

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 2683 AN: 113392 Hom.: 67 Cov.: 31

Gnomad AFR AF: 0.0700

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0116

Gnomad EAS AF: 0.00148

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00458

Gnomad MID AF: 0.0265

Gnomad NFE AF: 0.00491

Gnomad OTH AF: 0.0123

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

GnomAD4 genome AF: 0.0237 AC: 2687 AN: 113374 Hom.: 67 Cov.: 31 AF XY: 0.0225 AC XY: 1228 AN XY: 54488

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.0116

Gnomad4 EAS AF: 0.00148

Gnomad4 SAS AF: 0.00292

Gnomad4 FIN AF: 0.00458

Gnomad4 NFE AF: 0.00492

Gnomad4 OTH AF: 0.0123

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 01, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1179358669; hg19: chr1-61543524;