3-131504119-C-T

Position:

• chr3-131504119-C-T

Variant summary

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

The ENST00000655300.1(ENSG00000248468):​n.117+1415C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,144 control chromosomes in the GnomAD database, including 42,791 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 0.74 (42791 hom., cov: 32)
• Consequence: ENSG00000248468 ENST00000655300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

ENSG00000248468 (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 (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374114	XR_007096087.1	n.176+1035C>T		intron_variant
LOC105374114	XR_924495.4	n.176+1035C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248468	ENST00000655300.1	n.117+1415C>T		intron_variant
ENSG00000248468	ENST00000655982.1	n.55+1021C>T		intron_variant
ENSG00000248468	ENST00000660541.1	n.146+1025C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112311 AN: 152026 Hom.: 42734 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.739 AC: 112418 AN: 152144 Hom.: 42791 Cov.: 32 AF XY: 0.731 AC XY: 54344 AN XY: 74362

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.743

Alfa AF: 0.703 Hom.: 6194

Bravo AF: 0.738

Asia WGS AF: 0.545 AC: 1898 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	0.31
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9843898; hg19: chr3-131222963;