rs1163085

Positions:

• chr10-103279484-G-A

Variant summary

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

The NM_032727.4(INA):​c.1065+1208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,008 control chromosomes in the GnomAD database, including 31,521 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 0.64 (31521 hom., cov: 32)
• Consequence: INA NM_032727.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

Genes affected

INA (HGNC:6057): (internexin neuronal intermediate filament protein alpha) Neurofilaments are type IV intermediate filament heteropolymers composed of light, medium, and heavy chains. Neurofilaments comprise the axoskeleton and they functionally maintain the neuronal caliber. They may also play a role in intracellular transport to axons and dendrites. This gene is a member of the intermediate filament family and is involved in the morphogenesis of neurons. [provided by RefSeq, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INA	NM_032727.4	c.1065+1208G>A		intron_variant		ENST00000369849.9	NP_116116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INA	ENST00000369849.9	c.1065+1208G>A		intron_variant		1	NM_032727.4	ENSP00000358865	P1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97655 AN: 151890 Hom.: 31499 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.643 AC: 97720 AN: 152008 Hom.: 31521 Cov.: 32 AF XY: 0.644 AC XY: 47812 AN XY: 74294

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.633

Alfa AF: 0.644 Hom.: 42955

Bravo AF: 0.630

Asia WGS AF: 0.627 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.65

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: rs1163085; hg19: chr10-105039241;