chr5-7908246-C-G

Position:

• chr5-7908246-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058683.1(LOC124900936):​n.3604C>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 0.817 in 152,046 control chromosomes in the GnomAD database, including 51,287 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 0.82 (51287 hom., cov: 32)
• Consequence: LOC124900936 XR_007058683.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

LOC124900936 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900936	XR_007058683.1	n.3604C>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124087 AN: 151928 Hom.: 51236 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.817 AC: 124208 AN: 152046 Hom.: 51287 Cov.: 32 AF XY: 0.813 AC XY: 60441 AN XY: 74298

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.803

Alfa AF: 0.732 Hom.: 2147

Bravo AF: 0.817

Asia WGS AF: 0.661 AC: 2299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs327588; hg19: chr5-7908359;