rs4663098

chr2-127115459-T-Cchr2-127115459-T-G

Variant summary

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

The XR_923311.4(LOC105373605):n.672-804T>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 0.774 in 151,854 control chromosomes in the GnomAD database, including 45,663 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 0.77 (45663 hom., cov: 29)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373605	XR_923311.4	n.672-804T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117369 AN: 151738 Hom.: 45602 Cov.: 29

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.774 AC: 117493 AN: 151854 Hom.: 45663 Cov.: 29 AF XY: 0.771 AC XY: 57158 AN XY: 74170

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.750

Alfa AF: 0.767 Hom.: 91796

Bravo AF: 0.768

Asia WGS AF: 0.753 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.0
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4663098; hg19: chr2-127873035;