rs882020

Positions:

• chr7-44139144-C-T

Variant summary

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

The NM_021223.3(MYL7):​c.427-122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 719,804 control chromosomes in the GnomAD database, including 8,902 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 0.16 (1962 hom., cov: 33)
  • Exomes 𝑓: 0.15 (6940 hom.)
• Consequence: MYL7 NM_021223.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

MYL7 (HGNC:21719): (myosin light chain 7) Predicted to enable calcium ion binding activity. Located in A band. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYL7	NM_021223.3	c.427-122G>A		intron_variant		ENST00000223364.7	NP_067046.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYL7	ENST00000223364.7	c.427-122G>A		intron_variant		1	NM_021223.3	ENSP00000223364	P1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24038 AN: 152054 Hom.: 1962 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.153 AC: 86875 AN: 567632 Hom.: 6940 AF XY: 0.155 AC XY: 46351 AN XY: 299730

Gnomad4 AFR exome AF: 0.180

Gnomad4 AMR exome AF: 0.180

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.153

Gnomad4 SAS exome AF: 0.190

Gnomad4 FIN exome AF: 0.168

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.149

GnomAD4 genome AF: 0.158 AC: 24040 AN: 152172 Hom.: 1962 Cov.: 33 AF XY: 0.161 AC XY: 11946 AN XY: 74386

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.147

Alfa AF: 0.155 Hom.: 617

Bravo AF: 0.158

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.49

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: rs882020; hg19: chr7-44178743;