rs9378540

Positions:

• chr6-8335142-A-G

Variant summary

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

The ENST00000642149.1(ENSG00000232234):​n.586-7183A>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 0.288 in 152,122 control chromosomes in the GnomAD database, including 6,631 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 0.29 (6631 hom., cov: 32)
• Consequence: ENST00000642149.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 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
	ENST00000642149.1	n.586-7183A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43745 AN: 152004 Hom.: 6617 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.0378

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.288 AC: 43786 AN: 152122 Hom.: 6631 Cov.: 32 AF XY: 0.279 AC XY: 20775 AN XY: 74372

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.0380

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.326

Alfa AF: 0.286 Hom.: 1021

Bravo AF: 0.298

Asia WGS AF: 0.179 AC: 623 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9378540; hg19: chr6-8335375;