rs7821500

Variant names:

• chr8-27594527-T-G
• rs7821500
• ENST00000774578.1:n.169+1915T>G

Variant summary

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

The ENST00000774578.1(ENSG00000300853):​n.169+1915T>G variant causes a intron 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: ENSG00000300853 ENST00000774578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 2 publications found

Genes affected

ENSG00000300853 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774578.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300853	ENST00000774578.1		n.169+1915T>G		intron	N/A
	ENSG00000300853	ENST00000774579.1		n.284+1228T>G		intron	N/A
	ENSG00000300853	ENST00000774580.1		n.128+1269T>G		intron	N/A

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

African (AFR) AF: 0.511 AC: 21179 AN: 41408

American (AMR) AF: 0.331 AC: 5056 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1481 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2086 AN: 5144

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2014 AN: 10580

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21038 AN: 67970

Other (OTH) AF: 0.370 AC: 779 AN: 2108

Alfa AF: 0.362 Hom.: 1595

Bravo AF: 0.386

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7821500;

hg19: chr8-27452044;