rs1344189

Variant names:

• chr3-40207753-C-T
• rs1344189
• NM_015460.4:c.1666-2101C>T

Variant summary

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

The NM_015460.4(MYRIP):​c.1666-2101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,990 control chromosomes in the GnomAD database, including 16,750 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 0.46 (16750 hom., cov: 33)
• Consequence: MYRIP NM_015460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 5 publications found

Genes affected

MYRIP (HGNC:19156): (myosin VIIA and Rab interacting protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be involved in positive regulation of insulin secretion. Predicted to be located in actin cytoskeleton; dense core granule; and perinuclear region of cytoplasm. Predicted to be part of exocyst. Predicted to be active in cortical actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ENTPD3-AS1 (HGNC:):

EIF1B-AS1 (HGNC:44555): (EIF1B antisense RNA 1)

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 = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015460.4. 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
	MYRIP	NM_015460.4	MANE Select	c.1666-2101C>T		intron	N/A	NP_056275.2	Q8NFW9-1
	MYRIP	NM_001284423.2		c.1666-2101C>T		intron	N/A	NP_001271352.1	Q8NFW9-1
	MYRIP	NM_001284424.2		c.1666-2101C>T		intron	N/A	NP_001271353.1	Q8NFW9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYRIP	ENST00000302541.11	TSL:1 MANE Select	c.1666-2101C>T		intron	N/A	ENSP00000301972.6	Q8NFW9-1
	MYRIP	ENST00000444716.5	TSL:1	c.1666-2101C>T		intron	N/A	ENSP00000398665.1	Q8NFW9-1
	MYRIP	ENST00000396217.7	TSL:1	c.1399-2101C>T		intron	N/A	ENSP00000379519.3	Q8NFW9-6

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69295 AN: 151872 Hom.: 16740 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.456 AC: 69346 AN: 151990 Hom.: 16750 Cov.: 33 AF XY: 0.456 AC XY: 33896 AN XY: 74296

African (AFR) AF: 0.302 AC: 12539 AN: 41468

American (AMR) AF: 0.491 AC: 7498 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1319 AN: 3464

East Asian (EAS) AF: 0.265 AC: 1373 AN: 5176

South Asian (SAS) AF: 0.332 AC: 1605 AN: 4828

European-Finnish (FIN) AF: 0.582 AC: 6133 AN: 10534

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37453 AN: 67940

Other (OTH) AF: 0.428 AC: 904 AN: 2110

Alfa AF: 0.509 Hom.: 41783

Bravo AF: 0.442

Asia WGS AF: 0.289 AC: 1003 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.33
PhyloP100		-1.8
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: rs1344189; hg19: chr3-40249244;