rs1878916

Positions:

• chr3-40201699-G-A
• chr3-40201699-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015460.4(MYRIP):​c.1666-8155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 152,242 control chromosomes in the GnomAD database, including 68,284 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 0.95 (68284 hom., cov: 31)
• Consequence: MYRIP NM_015460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYRIP	NM_015460.4	c.1666-8155G>A		intron_variant		ENST00000302541.11
EIF1B-AS1	NR_033965.1	n.537-26977C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYRIP	ENST00000302541.11	c.1666-8155G>A		intron_variant		1	NM_015460.4	P1
EIF1B-AS1	ENST00000657703.1	n.91-83963C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143916 AN: 152124 Hom.: 68237 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.946 AC: 144022 AN: 152242 Hom.: 68284 Cov.: 31 AF XY: 0.947 AC XY: 70489 AN XY: 74436

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.944

Alfa AF: 0.965 Hom.: 11829

Bravo AF: 0.941

Asia WGS AF: 0.921 AC: 3202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.65

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: rs1878916; hg19: chr3-40243190;