rs6698914

Variant names:

• chr1-238600195-A-G
• rs6698914
• ENST00000716151.1:n.548-16946A>G

Variant summary

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

The ENST00000716151.1(ENSG00000234464):​n.548-16946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,270 control chromosomes in the GnomAD database, including 820 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 0.061 (820 hom., cov: 33)
• Consequence: ENSG00000234464 ENST00000716151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716151.1. 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	ENST00000716151.1		n.548-16946A>G		intron	N/A
	ENSG00000234464	ENST00000716155.1		n.473-13288A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9251 AN: 152152 Hom.: 814 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00223

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0609 AC: 9277 AN: 152270 Hom.: 820 Cov.: 33 AF XY: 0.0584 AC XY: 4346 AN XY: 74460

African (AFR) AF: 0.197 AC: 8195 AN: 41504

American (AMR) AF: 0.0436 AC: 668 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3468

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5186

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00223 AC: 152 AN: 68024

Other (OTH) AF: 0.0582 AC: 123 AN: 2114

Alfa AF: 0.0197 Hom.: 82

Bravo AF: 0.0704

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		0.019

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: rs6698914;

hg19: chr1-238763495;