rs4955316

Positions:

• chr3-30374120-T-G

Variant summary

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

The ENST00000691186.1(ENSG00000289450):​n.61+963T>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 0.138 in 151,848 control chromosomes in the GnomAD database, including 1,806 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 0.14 (1806 hom., cov: 32)
• Consequence: ENST00000691186.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927995	XR_427323.4	n.1150-15588T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691186.1	n.61+963T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20912 AN: 151730 Hom.: 1797 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.138 AC: 20942 AN: 151848 Hom.: 1806 Cov.: 32 AF XY: 0.142 AC XY: 10520 AN XY: 74188

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0857

Gnomad4 OTH AF: 0.121

Alfa AF: 0.109 Hom.: 603

Bravo AF: 0.155

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4955316; hg19: chr3-30415612;