rs4301033

chr3-150324831-G-A

Variant summary

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

The ENST00000692847.2(ENSG00000289524):n.63+6116C>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 0.113 in 152,172 control chromosomes in the GnomAD database, including 1,239 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 0.11 (1239 hom., cov: 32)
• Consequence: ENST00000692847.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986141	XR_001740958.1	n.1981+16432G>A		intron_variant, non_coding_transcript_variant
LOC107986141	XR_007096127.1	n.1981+16432G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692847.2	n.63+6116C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17233 AN: 152054 Hom.: 1237 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0789

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0556

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.113 AC: 17255 AN: 152172 Hom.: 1239 Cov.: 32 AF XY: 0.110 AC XY: 8190 AN XY: 74404

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0787

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0552

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0915

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0954 Hom.: 1356

Bravo AF: 0.120

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	11
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4301033; hg19: chr3-150042618;