XR_007060555.1:n.2947A>C

Variant names:

• chr7-138215387-T-G
• rs2352476
• XR_007060555.1:n.2947A>C

Variant summary

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

The XR_007060555.1(LOC124901754):​n.2947A>C 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 0.481 in 152,042 control chromosomes in the GnomAD database, including 18,870 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 0.48 (18870 hom., cov: 33)
• Consequence: LOC124901754 XR_007060555.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 6 publications found

Genes affected

LOC124901754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901754	XR_007060555.1	n.2947A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297982	ENST00000752300.1	n.605+208A>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72955 AN: 151924 Hom.: 18802 Cov.: 33

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.481 AC: 73087 AN: 152042 Hom.: 18870 Cov.: 33 AF XY: 0.482 AC XY: 35829 AN XY: 74312

African (AFR) AF: 0.647 AC: 26838 AN: 41472

American (AMR) AF: 0.557 AC: 8514 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.584 AC: 3019 AN: 5172

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4824

European-Finnish (FIN) AF: 0.434 AC: 4581 AN: 10556

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25336 AN: 67948

Other (OTH) AF: 0.452 AC: 953 AN: 2108

Alfa AF: 0.424 Hom.: 25343

Bravo AF: 0.497

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.20
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2352476; hg19: chr7-137900133;