3-54114743-G-A

Position:

• chr3-54114743-G-A

Variant summary

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

The ENST00000666932.1(ENSG00000286353):​n.1187+8314C>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 0.0957 in 152,194 control chromosomes in the GnomAD database, including 849 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 0.096 (849 hom., cov: 32)
• Consequence: ENST00000666932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909381	XR_007095914.1	n.386+8314C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666932.1	n.1187+8314C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14559 AN: 152074 Hom.: 847 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0651

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0957 AC: 14565 AN: 152194 Hom.: 849 Cov.: 32 AF XY: 0.0976 AC XY: 7258 AN XY: 74394

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.0576

Gnomad4 OTH AF: 0.0876

Alfa AF: 0.0669 Hom.: 568

Bravo AF: 0.0976

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2029118; hg19: chr3-54148770;