rs199055

Positions:

• chr6-23489889-A-G

Variant summary

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

The ENST00000690652.2(ENSG00000289368):​n.211-32219T>C 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 0.0605 in 152,178 control chromosomes in the GnomAD database, including 472 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 0.060 (472 hom., cov: 31)
• Consequence: ENST00000690652.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.401-32219T>C		intron_variant, non_coding_transcript_variant
LOC105374976	XR_007059501.1	n.379-32219T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000690652.2	n.211-32219T>C		intron_variant, non_coding_transcript_variant
	ENST00000700866.1	n.181-32219T>C		intron_variant, non_coding_transcript_variant
	ENST00000702216.1	n.203-32219T>C		intron_variant, non_coding_transcript_variant
	ENST00000702386.1	n.200-32219T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9178 AN: 152058 Hom.: 468 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0605 AC: 9201 AN: 152178 Hom.: 472 Cov.: 31 AF XY: 0.0631 AC XY: 4698 AN XY: 74400

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0299 Hom.: 287

Bravo AF: 0.0664

Asia WGS AF: 0.131 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199055; hg19: chr6-23490117;