chr7-138215387-T-G

Position:

• chr7-138215387-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124901754 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901754	XR_007060555.1	n.2947A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.452

Alfa AF: 0.430 Hom.: 5253

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2352476; hg19: chr7-137900133;