chr7-96089945-T-A

Variant names:

• chr7-96089945-T-A
• rs42064
• NM_001135556.2:c.1777-7538T>A

Variant summary

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

The NM_001135556.2(DYNC1I1):​c.1777-7538T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,984 control chromosomes in the GnomAD database, including 29,917 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 0.62 (29917 hom., cov: 32)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNC1I1	NM_001135556.2	c.1777-7538T>A		intron_variant	Intron 16 of 16	ENST00000447467.6	NP_001129028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNC1I1	ENST00000447467.6	c.1777-7538T>A		intron_variant	Intron 16 of 16	1	NM_001135556.2	ENSP00000392337.2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94397 AN: 151864 Hom.: 29907 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.621 AC: 94430 AN: 151984 Hom.: 29917 Cov.: 32 AF XY: 0.616 AC XY: 45766 AN XY: 74294

African (AFR) AF: 0.565 AC: 23419 AN: 41448

American (AMR) AF: 0.543 AC: 8292 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2594 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1942 AN: 5170

South Asian (SAS) AF: 0.486 AC: 2341 AN: 4820

European-Finnish (FIN) AF: 0.664 AC: 7013 AN: 10558

Middle Eastern (MID) AF: 0.748 AC: 217 AN: 290

European-Non Finnish (NFE) AF: 0.686 AC: 46585 AN: 67944

Other (OTH) AF: 0.647 AC: 1363 AN: 2106

Alfa AF: 0.553 Hom.: 1621

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.37
PhyloP100		-0.15
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: rs42064; hg19: chr7-95719257;