rs6692700

Variant names:

• chr1-238506476-C-A
• rs6692700
• ENST00000442726.1:n.216+17288C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-238506476-C-A
• chr1-238506476-C-G

Variant summary

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

The ENST00000442726.1(ENSG00000234464):​n.216+17288C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,952 control chromosomes in the GnomAD database, including 15,969 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 0.42 (15969 hom., cov: 33)
• Consequence: ENSG00000234464 ENST00000442726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 5 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442726.1. 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
	ENSG00000234464	ENST00000442726.1	TSL:2	n.216+17288C>A		intron	N/A
	ENSG00000234464	ENST00000716116.1		n.440-446C>A		intron	N/A
	ENSG00000234464	ENST00000716151.1		n.547+7186C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64135 AN: 151834 Hom.: 15939 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.423 AC: 64221 AN: 151952 Hom.: 15969 Cov.: 33 AF XY: 0.424 AC XY: 31461 AN XY: 74266

African (AFR) AF: 0.688 AC: 28526 AN: 41434

American (AMR) AF: 0.379 AC: 5782 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 911 AN: 3472

East Asian (EAS) AF: 0.568 AC: 2934 AN: 5168

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4826

European-Finnish (FIN) AF: 0.380 AC: 4013 AN: 10550

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19278 AN: 67940

Other (OTH) AF: 0.380 AC: 804 AN: 2114

Alfa AF: 0.376 Hom.: 1537

Bravo AF: 0.436

Asia WGS AF: 0.462 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.1
DANN	Benign	0.47
PhyloP100		-0.15

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: rs6692700;

hg19: chr1-238669776;