rs1084656

Positions:

• chr6-160760260-A-C
• chr6-160760260-A-T

Variant summary

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

The ENST00000659713.1(ENSG00000287558):​n.77+7154T>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 0.543 in 152,068 control chromosomes in the GnomAD database, including 23,305 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 0.54 (23305 hom., cov: 32)
• Consequence: ENST00000659713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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
	ENST00000659713.1	n.77+7154T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82558 AN: 151950 Hom.: 23276 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.543 AC: 82634 AN: 152068 Hom.: 23305 Cov.: 32 AF XY: 0.551 AC XY: 40918 AN XY: 74322

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.571

Alfa AF: 0.527 Hom.: 30870

Bravo AF: 0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1084656; hg19: chr6-161181292;