chr1-207421598-G-A

Variant names:

• chr1-207421598-G-A
• rs2135924
• ENST00000758268.1:n.268-2432G>A

Variant summary

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

The ENST00000758268.1(ENSG00000298838):​n.268-2432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,094 control chromosomes in the GnomAD database, including 2,677 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 0.19 (2677 hom., cov: 32)
• Consequence: ENSG00000298838 ENST00000758268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

Genes affected

ENSG00000298838 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758268.1. 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
	ENSG00000298838	ENST00000758268.1		n.268-2432G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28279 AN: 151976 Hom.: 2671 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.186 AC: 28306 AN: 152094 Hom.: 2677 Cov.: 32 AF XY: 0.183 AC XY: 13569 AN XY: 74348

African (AFR) AF: 0.186 AC: 7701 AN: 41488

American (AMR) AF: 0.155 AC: 2373 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3468

East Asian (EAS) AF: 0.105 AC: 545 AN: 5182

South Asian (SAS) AF: 0.165 AC: 797 AN: 4816

European-Finnish (FIN) AF: 0.167 AC: 1765 AN: 10560

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13720 AN: 67980

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.196 Hom.: 11046

Bravo AF: 0.186

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.7
DANN	Benign	0.90
PhyloP100		0.34

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: rs2135924;

hg19: chr1-207594943;

COSMIC: COSV60019705;