rs1488515

Variant names:

• chr7-96001884-T-G
• rs1488515
• NM_001135556.2:c.969+5811T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135556.2(DYNC1I1):​c.969+5811T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,188 control chromosomes in the GnomAD database, including 2,083 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 0.15 (2083 hom., cov: 32)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 8 publications found

Genes affected

DYNC1I1 (HGNC:2963): (dynein cytoplasmic 1 intermediate chain 1) Enables spectrin binding activity. Involved in vesicle transport along microtubule. Located in several cellular components, including kinetochore; recycling endosome; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNC1I1	NM_001135556.2	c.969+5811T>G		intron_variant	Intron 10 of 16	ENST00000447467.6	NP_001129028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.969+5811T>G		intron_variant	Intron 10 of 16	1	NM_001135556.2	ENSP00000392337.2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22871 AN: 152070 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.151 AC: 22911 AN: 152188 Hom.: 2083 Cov.: 32 AF XY: 0.154 AC XY: 11439 AN XY: 74396

African (AFR) AF: 0.111 AC: 4618 AN: 41528

American (AMR) AF: 0.177 AC: 2704 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1798 AN: 5170

South Asian (SAS) AF: 0.333 AC: 1602 AN: 4808

European-Finnish (FIN) AF: 0.108 AC: 1143 AN: 10598

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9985 AN: 67998

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.154 Hom.: 2033

Bravo AF: 0.153

Asia WGS AF: 0.288 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.77
PhyloP100		-0.46
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: rs1488515; hg19: chr7-95631196;