rs7821500

Positions:

• chr8-27594527-T-G

Variant summary

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

The XR_007060868.1(LOC124901919):​n.1397+1915T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,964 control chromosomes in the GnomAD database, including 11,166 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 0.37 (11166 hom., cov: 31)
• Consequence: LOC124901919 XR_007060868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

Genes affected

LOC124901919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901919	XR_007060868.1	n.1397+1915T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56053 AN: 151846 Hom.: 11149 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.369 AC: 56110 AN: 151964 Hom.: 11166 Cov.: 31 AF XY: 0.364 AC XY: 27048 AN XY: 74286

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.370

Alfa AF: 0.356 Hom.: 1494

Bravo AF: 0.386

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7821500; hg19: chr8-27452044;