rs9377831

chr6-58326972-A-G

Variant summary

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

The ENST00000641775.1(ENSG00000225096):n.457-109587A>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 0.118 in 152,078 control chromosomes in the GnomAD database, including 1,613 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 0.12 (1613 hom., cov: 32)
• Consequence: ENST00000641775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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
	ENST00000641775.1	n.457-109587A>G		intron_variant, non_coding_transcript_variant
	ENST00000641631.1	n.548+1424A>G		intron_variant, non_coding_transcript_variant
	ENST00000661843.1	n.525+1424A>G		intron_variant, non_coding_transcript_variant
	ENST00000670654.1	n.449-28173A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17934 AN: 151960 Hom.: 1612 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.118 AC: 17954 AN: 152078 Hom.: 1613 Cov.: 32 AF XY: 0.119 AC XY: 8878 AN XY: 74352

Gnomad4 AFR AF: 0.0748

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.0441

Gnomad4 FIN AF: 0.0790

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.128

Alfa AF: 0.130 Hom.: 338

Bravo AF: 0.135

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.7
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: rs9377831; hg19: chr6-58653250;