rs1876381

Positions:

• chr8-82046088-T-C

Variant summary

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

The ENST00000663058.1(ENSG00000254394):​n.306+12250T>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 0.201 in 151,332 control chromosomes in the GnomAD database, including 3,099 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 0.20 (3099 hom., cov: 28)
• Consequence: ENST00000663058.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663058.1	n.306+12250T>C		intron_variant, non_coding_transcript_variant
	ENST00000659043.1	n.59+12250T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30366 AN: 151214 Hom.: 3097 Cov.: 28

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.201 AC: 30382 AN: 151332 Hom.: 3099 Cov.: 28 AF XY: 0.199 AC XY: 14746 AN XY: 73952

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.197

Alfa AF: 0.217 Hom.: 600

Asia WGS AF: 0.137 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876381; hg19: chr8-82958323;