rs9296949

chr6-14597751-C-T

Variant summary

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

The ENST00000414740.2(ENSG00000229646):n.61-152G>A 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 0.0546 in 152,128 control chromosomes in the GnomAD database, including 396 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 0.055 (396 hom., cov: 32)
• Consequence: ENST00000414740.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928354	XR_241980.4	n.224-152G>A		intron_variant, non_coding_transcript_variant
LOC101928354	XR_001743992.2	n.362-152G>A		intron_variant, non_coding_transcript_variant
LOC101928354	XR_007059472.1	n.284-152G>A		intron_variant, non_coding_transcript_variant
LOC101928354	XR_926516.3	n.187-152G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000414740.2	n.61-152G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8288 AN: 152010 Hom.: 393 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0546 AC: 8302 AN: 152128 Hom.: 396 Cov.: 32 AF XY: 0.0575 AC XY: 4276 AN XY: 74376

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0545

Gnomad4 OTH AF: 0.0544

Alfa AF: 0.0538 Hom.: 46

Bravo AF: 0.0591

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.4
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296949; hg19: chr6-14597982;