rs2709376

Variant names:

• chr2-207525664-T-C
• rs2709376
• XR_007088060.1:n.528A>G

Variant summary

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

The XR_007088060.1(LOC124907970):​n.528A>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 0.885 in 152,240 control chromosomes in the GnomAD database, including 60,925 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 0.89 (60925 hom., cov: 32)
• Consequence: LOC124907970 XR_007088060.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907970	XR_007088060.1	n.528A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOSLID-AS1	ENST00000412387.5	n.181+2853A>G		intron_variant	Intron 2 of 4	4
MYOSLID-AS1	ENST00000418850.1	n.177+2853A>G		intron_variant	Intron 2 of 5	5
MYOSLID-AS1	ENST00000432413.3	n.163+2853A>G		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134708 AN: 152122 Hom.: 60888 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.885 AC: 134802 AN: 152240 Hom.: 60925 Cov.: 32 AF XY: 0.888 AC XY: 66100 AN XY: 74446

African (AFR) AF: 0.681 AC: 28263 AN: 41490

American (AMR) AF: 0.933 AC: 14275 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3236 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5189 AN: 5192

South Asian (SAS) AF: 0.985 AC: 4760 AN: 4832

European-Finnish (FIN) AF: 0.974 AC: 10340 AN: 10614

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65821 AN: 68020

Other (OTH) AF: 0.893 AC: 1885 AN: 2112

Alfa AF: 0.928 Hom.: 111574

Bravo AF: 0.874

Asia WGS AF: 0.970 AC: 3374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.048
DANN	Benign	0.46
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs2709376; hg19: chr2-208390388;