7-95813093-CTTTTT-CTTTT

Variant names:

• chr7-95813093-CT-C
• rs11452827
• NM_001135556.2:c.224-140delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001135556.2(DYNC1I1):​c.224-140delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,095,406 control chromosomes in the GnomAD database, including 1,148 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.098 (635 hom., cov: 0)
  • Exomes 𝑓: 0.13 (513 hom.)
• Consequence: DYNC1I1 NM_001135556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 0 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135556.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNC1I1	NM_001135556.2	MANE Select	c.224-140delT		intron	N/A	NP_001129028.1	O14576-2
	DYNC1I1	NM_004411.5		c.224-89delT		intron	N/A	NP_004402.1	O14576-1
	DYNC1I1	NM_001278421.2		c.224-89delT		intron	N/A	NP_001265350.1	O14576-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNC1I1	ENST00000447467.6	TSL:1 MANE Select	c.224-153delT		intron	N/A	ENSP00000392337.2	O14576-2
	DYNC1I1	ENST00000324972.10	TSL:1	c.224-102delT		intron	N/A	ENSP00000320130.6	O14576-1
	DYNC1I1	ENST00000457059.2	TSL:1	c.224-153delT		intron	N/A	ENSP00000412444.1	O14576-2

Frequencies

GnomAD3 genomes AF: 0.0978 AC: 13707 AN: 140210 Hom.: 638 Cov.: 0

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.0336

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0890

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.0731

GnomAD4 exome AF: 0.132 AC: 125795 AN: 955184 Hom.: 513 AF XY: 0.132 AC XY: 62809 AN XY: 475016

African (AFR) AF: 0.106 AC: 1963 AN: 18544

American (AMR) AF: 0.123 AC: 2096 AN: 17014

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 2455 AN: 16446

East Asian (EAS) AF: 0.142 AC: 3686 AN: 25948

South Asian (SAS) AF: 0.157 AC: 7610 AN: 48348

European-Finnish (FIN) AF: 0.155 AC: 4629 AN: 29776

Middle Eastern (MID) AF: 0.111 AC: 318 AN: 2860

European-Non Finnish (NFE) AF: 0.129 AC: 97813 AN: 756594

Other (OTH) AF: 0.132 AC: 5225 AN: 39654

GnomAD4 genome AF: 0.0977 AC: 13703 AN: 140222 Hom.: 635 Cov.: 0 AF XY: 0.101 AC XY: 6795 AN XY: 67504

African (AFR) AF: 0.0862 AC: 3286 AN: 38130

American (AMR) AF: 0.0975 AC: 1353 AN: 13878

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 382 AN: 3376

East Asian (EAS) AF: 0.122 AC: 590 AN: 4822

South Asian (SAS) AF: 0.136 AC: 608 AN: 4486

European-Finnish (FIN) AF: 0.137 AC: 972 AN: 7074

Middle Eastern (MID) AF: 0.0852 AC: 23 AN: 270

European-Non Finnish (NFE) AF: 0.0967 AC: 6320 AN: 65364

Other (OTH) AF: 0.0720 AC: 139 AN: 1930

Alfa AF: 0.0537 Hom.: 272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.36
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: rs11452827; hg19: chr7-95442405;