rs2308072

Positions:

• chr8-19232269-T-TAAGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_038919.1(LOC100128993):​n.504+3194_504+3195insCCTT variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18393 hom., cov: 0)
• Consequence: LOC100128993 NR_038919.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100128993	NR_038919.1	n.504+3194_504+3195insCCTT		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000520920.5	n.410+3194_410+3195insCCTT		intron_variant, non_coding_transcript_variant		4
	ENST00000517949.5	n.471+3194_471+3195insCCTT		intron_variant, non_coding_transcript_variant		3
	ENST00000518417.1	n.214+3194_214+3195insCCTT		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73655 AN: 151324 Hom.: 18373 Cov.: 0

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.487 AC: 73705 AN: 151442 Hom.: 18393 Cov.: 0 AF XY: 0.483 AC XY: 35726 AN XY: 73994

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.469

Alfa AF: 0.483 Hom.: 1932

Asia WGS AF: 0.354 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2308072; hg19: chr8-19089779;