chr4-99382344-G-T

Position:

• chr4-99382344-G-T

Variant summary

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

The XR_939020.3(LOC102723576):​n.1413+1148C>A 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 0.883 in 152,158 control chromosomes in the GnomAD database, including 59,475 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 0.88 (59475 hom., cov: 32)
• Consequence: LOC102723576 XR_939020.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

LOC102723576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723576	XR_939020.3	n.1413+1148C>A		intron_variant, non_coding_transcript_variant
LOC102723576	XR_001741777.2	n.1664C>A		non_coding_transcript_exon_variant	4/4
LOC102723576	XR_427569.4	n.2561C>A		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134205 AN: 152040 Hom.: 59428 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.883 AC: 134313 AN: 152158 Hom.: 59475 Cov.: 32 AF XY: 0.882 AC XY: 65592 AN XY: 74366

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.849

Alfa AF: 0.887 Hom.: 7459

Bravo AF: 0.877

Asia WGS AF: 0.833 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2851292; hg19: chr4-100303501;