rs6994682

chr8-100409570-T-C

Variant summary

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

The ENST00000664475.1(ENSG00000253824):n.120-27799A>G 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 0.3 in 152,090 control chromosomes in the GnomAD database, including 12,802 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 0.30 (12802 hom., cov: 32)
• Consequence: ENST00000664475.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664475.1	n.120-27799A>G		intron_variant, non_coding_transcript_variant
	ENST00000519844.2	n.152+1165A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000654832.1	n.180+4795A>G		intron_variant, non_coding_transcript_variant
	ENST00000657736.1	n.63+4795A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45495 AN: 151972 Hom.: 12760 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.300 AC: 45591 AN: 152090 Hom.: 12802 Cov.: 32 AF XY: 0.294 AC XY: 21849 AN XY: 74344

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.256

Alfa AF: 0.149 Hom.: 4270

Bravo AF: 0.325

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.1
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6994682; hg19: chr8-101421798;