rs6785385

Positions:

• chr3-81940699-A-G

Variant summary

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

The ENST00000670278.1(ENSG00000242009):​n.1291+1758A>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 0.534 in 151,784 control chromosomes in the GnomAD database, including 23,164 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 0.53 (23164 hom., cov: 31)
• Consequence: ENST00000670278.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513

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 = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377179	XR_940999.2	n.462+1758A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670278.1	n.1291+1758A>G		intron_variant, non_coding_transcript_variant
	ENST00000654999.1	n.1138+1758A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80925 AN: 151666 Hom.: 23142 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.534 AC: 80999 AN: 151784 Hom.: 23164 Cov.: 31 AF XY: 0.533 AC XY: 39526 AN XY: 74180

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.492

Alfa AF: 0.495 Hom.: 2423

Bravo AF: 0.551

Asia WGS AF: 0.588 AC: 2044 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6785385; hg19: chr3-81989850;