7-127509237-A-C

Variant names:

• chr7-127509237-A-C
• rs10487488
• XR_001745351.2:n.2293T>G

Variant summary

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

The XR_001745351.2(LOC105375490):​n.2293T>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,230 control chromosomes in the GnomAD database, including 892 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 0.11 (892 hom., cov: 32)
• Consequence: LOC105375490 XR_001745351.2 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923
• Publications: 7 publications found

Genes affected

LOC105375490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731796.1. 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
	ENSG00000295686	ENST00000731796.1		n.70-3871T>G		intron	N/A
	ENSG00000295686	ENST00000731797.1		n.355-23955T>G		intron	N/A
	ENSG00000295686	ENST00000731798.1		n.244-3871T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16025 AN: 152112 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.105 AC: 16030 AN: 152230 Hom.: 892 Cov.: 32 AF XY: 0.106 AC XY: 7864 AN XY: 74444

African (AFR) AF: 0.124 AC: 5150 AN: 41522

American (AMR) AF: 0.0820 AC: 1253 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3472

East Asian (EAS) AF: 0.0931 AC: 483 AN: 5188

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1370 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6838 AN: 68018

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0972 Hom.: 488

Bravo AF: 0.103

Asia WGS AF: 0.0950 AC: 333 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	18
DANN	Benign	0.69
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs10487488; hg19: chr7-127149291;