rs7723819

Variant names:

• chr5-111091649-G-A
• rs7723819
• ENST00000507269.3:n.46+421C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-111091649-G-A
• chr5-111091649-G-T

Variant summary

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

The ENST00000507269.3(ENSG00000253613):​n.46+421C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 153,656 control chromosomes in the GnomAD database, including 22,483 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 0.53 (22255 hom., cov: 32)
  • Exomes 𝑓: 0.50 (228 hom.)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253613	ENST00000507269.3	n.46+421C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80809 AN: 151906 Hom.: 22228 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.522

GnomAD4 exome AF: 0.504 AC: 822 AN: 1632 Hom.: 228 AF XY: 0.543 AC XY: 456 AN XY: 840

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.618

Gnomad4 EAS exome AF: 0.423

Gnomad4 SAS exome AF: 0.741

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.451

Gnomad4 OTH exome AF: 0.480

GnomAD4 genome AF: 0.532 AC: 80891 AN: 152024 Hom.: 22255 Cov.: 32 AF XY: 0.538 AC XY: 39990 AN XY: 74314

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.521

Alfa AF: 0.492 Hom.: 1740

Bravo AF: 0.530

Asia WGS AF: 0.534 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7723819; hg19: chr5-110427347;