rs284794

Variant names:

• chr4-99401872-T-A
• rs284794
• XR_001741777.2:n.387+961A>T

Variant summary

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

The XR_427569.4(LOC102723576):​n.1284+961A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0942 in 152,208 control chromosomes in the GnomAD database, including 719 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 0.094 (719 hom., cov: 32)
• Consequence: LOC102723576 XR_427569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.387+961A>T		intron_variant	Intron 3 of 3
LOC102723576	XR_427569.4	n.1284+961A>T		intron_variant	Intron 3 of 3
LOC102723576	XR_939020.3	n.1284+961A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0941 AC: 14315 AN: 152090 Hom.: 714 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.0942 AC: 14341 AN: 152208 Hom.: 719 Cov.: 32 AF XY: 0.0915 AC XY: 6812 AN XY: 74414

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0322

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0900

Gnomad4 OTH AF: 0.0951

Alfa AF: 0.0935 Hom.: 85

Bravo AF: 0.0938

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.89
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: rs284794; hg19: chr4-100323029;