rs618675

Variant names:

• chr1-34684573-T-C
• rs618675
• ENST00000666642.1:n.568+592A>G

Variant summary

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

The ENST00000666642.1(ENSG00000287703):​n.568+592A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,082 control chromosomes in the GnomAD database, including 4,289 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 0.23 (4289 hom., cov: 32)
• Consequence: ENSG00000287703 ENST00000666642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 8 publications found

Genes affected

ENSG00000287703 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666642.1. 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
	ENSG00000287703	ENST00000666642.1		n.568+592A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34931 AN: 151962 Hom.: 4275 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.230 AC: 34966 AN: 152082 Hom.: 4289 Cov.: 32 AF XY: 0.231 AC XY: 17204 AN XY: 74334

African (AFR) AF: 0.280 AC: 11610 AN: 41454

American (AMR) AF: 0.322 AC: 4919 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.144 AC: 747 AN: 5176

South Asian (SAS) AF: 0.185 AC: 892 AN: 4820

European-Finnish (FIN) AF: 0.228 AC: 2409 AN: 10576

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13143 AN: 67986

Other (OTH) AF: 0.236 AC: 498 AN: 2108

Alfa AF: 0.221 Hom.: 1842

Bravo AF: 0.243

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	14
DANN	Benign	0.68
PhyloP100		0.23

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: rs618675;

hg19: chr1-35150174;