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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904565	XR_007066966.1	n.65-16946A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234464	ENST00000716151.1	n.548-16946A>G		intron_variant	Intron 5 of 7
ENSG00000234464	ENST00000716155.1	n.473-13288A>G		intron_variant	Intron 5 of 8

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 v4.3

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

Other links and lift over

dbSNP: rs6698914; hg19: chr1-238763495;