rs1084656

Variant names:

• chr6-160760260-A-C
• rs1084656
• ENST00000659713.1:n.77+7154T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659713.1(ENSG00000287558):​n.77+7154T>G variant causes a intron 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: ENSG00000287558 ENST00000659713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 6 publications found

Genes affected

ENSG00000287558 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287558	ENST00000659713.1	n.77+7154T>G		intron_variant	Intron 1 of 1
ENSG00000287558	ENST00000785027.1	n.191-5302T>G		intron_variant	Intron 2 of 3
ENSG00000287558	ENST00000785028.1	n.157-4805T>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.460 AC: 19083 AN: 41474

American (AMR) AF: 0.656 AC: 10035 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3466

East Asian (EAS) AF: 0.977 AC: 5057 AN: 5178

South Asian (SAS) AF: 0.682 AC: 3290 AN: 4826

European-Finnish (FIN) AF: 0.530 AC: 5590 AN: 10556

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35966 AN: 67960

Other (OTH) AF: 0.571 AC: 1207 AN: 2112

Alfa AF: 0.530 Hom.: 49932

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1084656; hg19: chr6-161181292;