rs34858744

Variant names:

• chr1-207319604-G-C
• rs34858744
• ENST00000740658.1:n.116+2082C>G

Variant summary

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

The ENST00000740658.1(ENSG00000296591):​n.116+2082C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 152,256 control chromosomes in the GnomAD database, including 206 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 0.042 (206 hom., cov: 31)
• Consequence: ENSG00000296591 ENST00000740658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 0 publications found

Genes affected

ENSG00000296591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985251	XR_007066837.1	n.444+2082C>G		intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1	n.444+2082C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296591	ENST00000740658.1	n.116+2082C>G		intron_variant	Intron 1 of 2
ENSG00000296591	ENST00000740659.1	n.96+2082C>G		intron_variant	Intron 1 of 4
ENSG00000296591	ENST00000740660.1	n.89+2082C>G		intron_variant	Intron 1 of 3
ENSG00000296591	ENST00000740661.1	n.86+2082C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6318 AN: 152138 Hom.: 206 Cov.: 31

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0415 AC: 6326 AN: 152256 Hom.: 206 Cov.: 31 AF XY: 0.0407 AC XY: 3032 AN XY: 74434

African (AFR) AF: 0.0960 AC: 3985 AN: 41518

American (AMR) AF: 0.0256 AC: 391 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00331 AC: 16 AN: 4830

European-Finnish (FIN) AF: 0.0365 AC: 387 AN: 10608

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0210 AC: 1427 AN: 68018

Other (OTH) AF: 0.0360 AC: 76 AN: 2114

Alfa AF: 0.0320 Hom.: 20

Bravo AF: 0.0445

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.6
DANN	Benign	0.69
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs34858744; hg19: chr1-207492949;