XR_007088059.1:n.415A>T

Variant names:

• chr2-207529183-T-A
• rs2709377
• XR_007088059.1:n.415A>T

Variant summary

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

The XR_007088059.1(LOC124907970):​n.415A>T 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 0.157 in 152,046 control chromosomes in the GnomAD database, including 2,084 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 (2084 hom., cov: 30)
• Consequence: LOC124907970 XR_007088059.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 4 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYOSLID-AS1	ENST00000412387.5	TSL:4	n.84+529A>T		intron	N/A
	MYOSLID-AS1	ENST00000418850.1	TSL:5	n.80+529A>T		intron	N/A
	MYOSLID-AS1	ENST00000432413.3	TSL:3	n.66+529A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23946 AN: 151928 Hom.: 2084 Cov.: 30

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.157 AC: 23947 AN: 152046 Hom.: 2084 Cov.: 30 AF XY: 0.153 AC XY: 11370 AN XY: 74346

African (AFR) AF: 0.133 AC: 5497 AN: 41462

American (AMR) AF: 0.134 AC: 2047 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0614 AC: 296 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1542 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13285 AN: 67948

Other (OTH) AF: 0.155 AC: 327 AN: 2108

Alfa AF: 0.177 Hom.: 312

Bravo AF: 0.154

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2709377; hg19: chr2-208393907;