rs74844716

Variant names:

• chr2-207527491-T-C
• rs74844716
• XR_007088059.1:n.2008A>G

Variant summary

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

The XR_007088059.1(LOC124907970):​n.2008A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,240 control chromosomes in the GnomAD database, including 704 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 0.082 (704 hom., cov: 32)
• Consequence: LOC124907970 XR_007088059.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 1 publications found

Genes affected

LOC124907970 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412387.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOSLID-AS1	ENST00000412387.5	TSL:4	n.181+1026A>G		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.177+1026A>G		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.163+1026A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12406 AN: 152122 Hom.: 703 Cov.: 32

Gnomad AFR AF: 0.0203

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0815 AC: 12409 AN: 152240 Hom.: 704 Cov.: 32 AF XY: 0.0792 AC XY: 5894 AN XY: 74426

African (AFR) AF: 0.0202 AC: 838 AN: 41546

American (AMR) AF: 0.105 AC: 1605 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0882 AC: 426 AN: 4832

European-Finnish (FIN) AF: 0.110 AC: 1166 AN: 10586

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7904 AN: 68010

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

Alfa AF: 0.105 Hom.: 123

Bravo AF: 0.0791

Asia WGS AF: 0.0430 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.80
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs74844716; hg19: chr2-208392215;