rs2709377

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907970	XR_007088059.1	n.415A>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124907970	XR_007088060.1	n.162+253A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOSLID-AS1	ENST00000412387.5	n.84+529A>T		intron_variant	Intron 1 of 4	4
MYOSLID-AS1	ENST00000418850.1	n.80+529A>T		intron_variant	Intron 1 of 5	5
MYOSLID-AS1	ENST00000432413.3	n.66+529A>T		intron_variant	Intron 1 of 5	3

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 v4.3

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;