chr4-31716823-A-C

Position:

• chr4-31716823-A-C

Variant summary

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

The XR_925555.1(LOC105374566):​n.193+302T>G 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 0.103 in 151,738 control chromosomes in the GnomAD database, including 1,076 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 0.10 (1076 hom., cov: 32)
• Consequence: LOC105374566 XR_925555.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

LOC105374566 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374566	XR_925555.1	n.193+302T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15658 AN: 151620 Hom.: 1076 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15662 AN: 151738 Hom.: 1076 Cov.: 32 AF XY: 0.104 AC XY: 7697 AN XY: 74154

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0507

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.109

Alfa AF: 0.138 Hom.: 756

Bravo AF: 0.0940

Asia WGS AF: 0.0840 AC: 293 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489007; hg19: chr4-31718445;