rs1344189

Positions:

• chr3-40207753-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYRIP	NM_015460.4	c.1666-2101C>T		intron_variant		ENST00000302541.11	NP_056275.2
EIF1B-AS1	NR_033965.1	n.537-33031G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYRIP	ENST00000302541.11	c.1666-2101C>T		intron_variant		1	NM_015460.4	ENSP00000301972	P1
EIF1B-AS1	ENST00000657703.1	n.91-90017G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.428

Alfa AF: 0.523 Hom.: 28954

Bravo AF: 0.442

Asia WGS AF: 0.289 AC: 1003 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344189; hg19: chr3-40249244;