6-88185158-C-G

Variant summary

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

The ENST00000648572.1(ENSG00000234426):n.991-6724G>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 0.0834 in 152,166 control chromosomes in the GnomAD database, including 636 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 0.083 (636 hom., cov: 32)
• Consequence: ENST00000648572.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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
	ENST00000648572.1	n.991-6724G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12697 AN: 152048 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0834 AC: 12698 AN: 152166 Hom.: 636 Cov.: 32 AF XY: 0.0821 AC XY: 6111 AN XY: 74400

Gnomad4 AFR AF: 0.0333

Gnomad4 AMR AF: 0.0585

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0810

Alfa AF: 0.0390 Hom.: 40

Bravo AF: 0.0770

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.23
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884830; hg19: chr6-88894877;