rs6687840

Variant names:

• chr1-159372649-C-T
• rs6687840
• ENST00000431862.1:n.228-8140G>A

Variant summary

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

The ENST00000431862.1(ENSG00000228560):​n.228-8140G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,000 control chromosomes in the GnomAD database, including 20,335 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 0.47 (20335 hom., cov: 32)
• Consequence: ENSG00000228560 ENST00000431862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 16 publications found

Genes affected

ENSG00000228560 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431862.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228560	ENST00000431862.1	TSL:1	n.228-8140G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70576 AN: 151882 Hom.: 20288 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.465 AC: 70680 AN: 152000 Hom.: 20335 Cov.: 32 AF XY: 0.464 AC XY: 34458 AN XY: 74278

African (AFR) AF: 0.823 AC: 34119 AN: 41470

American (AMR) AF: 0.443 AC: 6759 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3468

East Asian (EAS) AF: 0.336 AC: 1734 AN: 5162

South Asian (SAS) AF: 0.295 AC: 1422 AN: 4816

European-Finnish (FIN) AF: 0.349 AC: 3680 AN: 10542

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20785 AN: 67954

Other (OTH) AF: 0.401 AC: 846 AN: 2108

Alfa AF: 0.357 Hom.: 38232

Bravo AF: 0.488

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.49
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6687840;

hg19: chr1-159342439;