rs1891284

Positions:

• chr6-14651937-C-T

Variant summary

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

The ENST00000702111.1(ENSG00000289958):​n.37+4846G>A 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 0.394 in 152,030 control chromosomes in the GnomAD database, including 12,634 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 0.39 (12634 hom., cov: 32)
• Consequence: ENST00000702111.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928354	XR_241980.4	n.47-7868G>A		intron_variant, non_coding_transcript_variant
LOC101928354	XR_001743992.2	n.47-7868G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702111.1	n.37+4846G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59856 AN: 151912 Hom.: 12622 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.394 AC: 59896 AN: 152030 Hom.: 12634 Cov.: 32 AF XY: 0.395 AC XY: 29333 AN XY: 74318

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.448

Alfa AF: 0.442 Hom.: 8969

Bravo AF: 0.399

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.89
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891284; hg19: chr6-14652168;