chr1-238358337-G-T

Variant names:

• chr1-238358337-G-T
• rs11583706
• ENST00000665394.1:n.325+32063G>T

Variant summary

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

The ENST00000665394.1(ENSG00000234464):​n.325+32063G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,050 control chromosomes in the GnomAD database, including 2,171 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 0.17 (2171 hom., cov: 33)
• Consequence: ENSG00000234464 ENST00000665394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373220	XR_949308.3	n.264+32063G>T		intron_variant	Intron 3 of 4
LOC105373220	XR_949311.3	n.190+32504G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234464	ENST00000665394.1	n.325+32063G>T		intron_variant	Intron 4 of 4
ENSG00000234464	ENST00000716116.1	n.130+32063G>T		intron_variant	Intron 1 of 4
ENSG00000234464	ENST00000716147.1	n.500+32063G>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25641 AN: 151932 Hom.: 2167 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.169 AC: 25664 AN: 152050 Hom.: 2171 Cov.: 33 AF XY: 0.172 AC XY: 12815 AN XY: 74314

African (AFR) AF: 0.187 AC: 7755 AN: 41486

American (AMR) AF: 0.199 AC: 3043 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3470

East Asian (EAS) AF: 0.126 AC: 653 AN: 5164

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2260 AN: 10548

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9466 AN: 67980

Other (OTH) AF: 0.178 AC: 376 AN: 2112

Alfa AF: 0.152 Hom.: 945

Bravo AF: 0.173

Asia WGS AF: 0.228 AC: 790 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.18
PhyloP100		0.0080

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11583706; hg19: chr1-238521637; COSMIC: COSV60042506;