rs1163085

Variant names:

• chr10-103279484-G-A
• rs1163085
• NM_032727.4:c.1065+1208G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
INA	NM_032727.4	c.1065+1208G>A		intron_variant	Intron 1 of 2	ENST00000369849.9	NP_116116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INA	ENST00000369849.9	c.1065+1208G>A		intron_variant	Intron 1 of 2	1	NM_032727.4	ENSP00000358865.4

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

African (AFR) AF: 0.644 AC: 26710 AN: 41462

American (AMR) AF: 0.594 AC: 9061 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2236 AN: 3468

East Asian (EAS) AF: 0.593 AC: 3067 AN: 5170

South Asian (SAS) AF: 0.693 AC: 3335 AN: 4814

European-Finnish (FIN) AF: 0.686 AC: 7240 AN: 10554

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43952 AN: 67962

Other (OTH) AF: 0.633 AC: 1336 AN: 2110

Alfa AF: 0.644 Hom.: 54021

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
PhyloP100		-0.022
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1163085; hg19: chr10-105039241;