rs882020

Variant names:

• chr7-44139144-C-T
• rs882020
• NM_021223.3:c.427-122G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021223.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYL7	NM_021223.3	MANE Select	c.427-122G>A		intron	N/A	NP_067046.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYL7	ENST00000223364.7	TSL:1 MANE Select	c.427-122G>A		intron	N/A	ENSP00000223364.3
	MYL7	ENST00000458240.5	TSL:1	c.346-122G>A		intron	N/A	ENSP00000403360.1
	MYL7	ENST00000457314.5	TSL:3	c.493-122G>A		intron	N/A	ENSP00000389202.1

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

African (AFR) AF: 0.180 AC: 2742 AN: 15228

American (AMR) AF: 0.180 AC: 4772 AN: 26556

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 2428 AN: 16102

East Asian (EAS) AF: 0.153 AC: 4912 AN: 32134

South Asian (SAS) AF: 0.190 AC: 10324 AN: 54224

European-Finnish (FIN) AF: 0.168 AC: 5918 AN: 35234

Middle Eastern (MID) AF: 0.146 AC: 376 AN: 2582

European-Non Finnish (NFE) AF: 0.143 AC: 50867 AN: 355198

Other (OTH) AF: 0.149 AC: 4536 AN: 30374

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

African (AFR) AF: 0.177 AC: 7341 AN: 41520

American (AMR) AF: 0.175 AC: 2680 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 491 AN: 3468

East Asian (EAS) AF: 0.171 AC: 883 AN: 5176

South Asian (SAS) AF: 0.195 AC: 944 AN: 4832

European-Finnish (FIN) AF: 0.157 AC: 1664 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9587 AN: 67984

Other (OTH) AF: 0.147 AC: 311 AN: 2110

Alfa AF: 0.154 Hom.: 967

Bravo AF: 0.158

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.49
PhyloP100		0.23
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: rs882020; hg19: chr7-44178743;