chr4-121490372-G-T

Position:

• chr4-121490372-G-T

Variant summary

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

The XR_001741806.2(LOC107986309):​n.416+327G>T 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 0.645 in 151,886 control chromosomes in the GnomAD database, including 32,225 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 0.64 (32225 hom., cov: 32)
• Consequence: LOC107986309 XR_001741806.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

Genes affected

LOC107986309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986309	XR_001741806.2	n.416+327G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97856 AN: 151768 Hom.: 32184 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.645 AC: 97941 AN: 151886 Hom.: 32225 Cov.: 32 AF XY: 0.643 AC XY: 47749 AN XY: 74236

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.600

Alfa AF: 0.616 Hom.: 6027

Bravo AF: 0.642

Asia WGS AF: 0.629 AC: 2183 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
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: rs1513721; hg19: chr4-122411527;