rs9321765

Positions:

• chr6-140274607-T-C

Variant summary

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

The ENST00000683950.1(ENSG00000288714):​n.202-40223T>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 0.19 in 151,754 control chromosomes in the GnomAD database, including 3,008 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 0.19 (3008 hom., cov: 32)
• Consequence: ENST00000683950.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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
	ENST00000683950.1	n.202-40223T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28821 AN: 151636 Hom.: 3007 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.190 AC: 28838 AN: 151754 Hom.: 3008 Cov.: 32 AF XY: 0.190 AC XY: 14107 AN XY: 74180

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.188

Alfa AF: 0.189 Hom.: 364

Bravo AF: 0.187

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
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: rs9321765; hg19: chr6-140595744;