rs3746444

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate

The NM_020884(MYH7B):c.1977+138A>C variant causes a intron change. The variant was absent in control chromosomes in GnomAD Genomes project. 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: not found (cov: 32)

Consequence

MYH7B
NM_020884 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.64

Links

MYH7B (HGNC:15906):

MIR499A (HGNC:32133):

MIR499B (HGNC:41640):

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2

Very rare variant; Number of alleles below threshold, Median coverage is 32.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
MYH7B	NM_020884.7 linkuse as main transcript	c.1977+138A>C	intron_variant		ENST00000262873.13
MIR499A	NR_030223.1 linkuse as main transcript	n.73A>C	non_coding_transcript_exon_variant	1/1
MIR499B	NR_039912.1 linkuse as main transcript	n.25T>G	non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
MYH7B	ENST00000262873.13 linkuse as main transcript	c.1977+138A>C	intron_variant		1	NM_020884.7	P1
MIR499A	ENST00000384903.1 linkuse as main transcript	n.73A>C	mature_miRNA_variant	1/1
MIR499B	ENST00000636498.1 linkuse as main transcript	n.25T>G	mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

Cadd

Benign

Dann

Benign

0.87

Splicing

Find out SpliceAI and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over