rs2709376

chr2-207525664-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124907970 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124907970	XR_007088060.1	n.528A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412387.5	n.181+2853A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.177+2853A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.893

Alfa AF: 0.949 Hom.: 81953

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2709376; hg19: chr2-208390388;