4-99393381-C-T

Variant names:

• chr4-99393381-C-T
• rs1442487
• XR_001741777.2:n.387+9452G>A

Variant summary

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

The XR_427569.4(LOC102723576):​n.1284+9452G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,710 control chromosomes in the GnomAD database, including 11,186 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 (11186 hom., cov: 31)
• Consequence: LOC102723576 XR_427569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.387+9452G>A		intron_variant	Intron 3 of 3
LOC102723576	XR_427569.4	n.1284+9452G>A		intron_variant	Intron 3 of 3
LOC102723576	XR_939020.3	n.1284+9452G>A		intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56187 AN: 151592 Hom.: 11163 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.371 AC: 56252 AN: 151710 Hom.: 11186 Cov.: 31 AF XY: 0.380 AC XY: 28155 AN XY: 74096

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.347

Alfa AF: 0.336 Hom.: 1448

Bravo AF: 0.368

Asia WGS AF: 0.599 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1442487; hg19: chr4-100314538;