rs1878916

Variant names:

• chr3-40201699-G-A
• rs1878916
• NM_015460.4:c.1666-8155G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_015460.4(MYRIP):​c.1666-8155G>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
• Publications: 0 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.97 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.1666-8155G>A		intron	N/A	NP_056275.2	Q8NFW9-1
	MYRIP	NM_001284423.2		c.1666-8155G>A		intron	N/A	NP_001271352.1	Q8NFW9-1
	MYRIP	NM_001284424.2		c.1666-8155G>A		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.1666-8155G>A		intron	N/A	ENSP00000301972.6	Q8NFW9-1
	MYRIP	ENST00000444716.5	TSL:1	c.1666-8155G>A		intron	N/A	ENSP00000398665.1	Q8NFW9-1
	MYRIP	ENST00000396217.7	TSL:1	c.1399-8155G>A		intron	N/A	ENSP00000379519.3	Q8NFW9-6

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

African (AFR) AF: 0.876 AC: 36356 AN: 41502

American (AMR) AF: 0.963 AC: 14735 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3349 AN: 3470

East Asian (EAS) AF: 0.952 AC: 4933 AN: 5182

South Asian (SAS) AF: 0.940 AC: 4527 AN: 4818

European-Finnish (FIN) AF: 0.991 AC: 10522 AN: 10618

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66418 AN: 68034

Other (OTH) AF: 0.944 AC: 1994 AN: 2112

Alfa AF: 0.962 Hom.: 12126

Bravo AF: 0.941

Asia WGS AF: 0.921 AC: 3202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.65
PhyloP100		-1.9
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: rs1878916; hg19: chr3-40243190;