rs7427021

chr3-164044176-A-G

Variant summary

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

The XR_001740997.2(LOC102724419):n.1322-13480T>C 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 0.511 in 151,814 control chromosomes in the GnomAD database, including 20,446 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 0.51 (20446 hom., cov: 32)
• Consequence: LOC102724419 XR_001740997.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416

Genes affected

LOC102724419 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724419	XR_001740997.2	n.1322-13480T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77523 AN: 151694 Hom.: 20400 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.511 AC: 77628 AN: 151814 Hom.: 20446 Cov.: 32 AF XY: 0.510 AC XY: 37806 AN XY: 74176

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.513

Alfa AF: 0.463 Hom.: 28868

Bravo AF: 0.516

Asia WGS AF: 0.577 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	9.7
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7427021; hg19: chr3-163761964;