chr1-175153430-A-G

Variant names:

• chr1-175153430-A-G
• rs4650707
• ENST00000785604.1:n.534A>G

Variant summary

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

The ENST00000785604.1(ENSG00000302295):​n.534A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.975 in 152,366 control chromosomes in the GnomAD database, including 72,456 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 0.98 (72456 hom., cov: 33)
• Consequence: ENSG00000302295 ENST00000785604.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 1 publications found

Genes affected

ENSG00000302295 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302295	ENST00000785604.1	n.534A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000302295	ENST00000785605.1	n.353A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000302295	ENST00000785606.1	n.422A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000302295	ENST00000785607.1	n.556A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.975 AC: 148463 AN: 152248 Hom.: 72398 Cov.: 33

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.961

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.975 AC: 148580 AN: 152366 Hom.: 72456 Cov.: 33 AF XY: 0.977 AC XY: 72824 AN XY: 74512

African (AFR) AF: 0.993 AC: 41303 AN: 41592

American (AMR) AF: 0.971 AC: 14871 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3409 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5149 AN: 5178

South Asian (SAS) AF: 0.992 AC: 4795 AN: 4834

European-Finnish (FIN) AF: 0.983 AC: 10450 AN: 10626

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.961 AC: 65404 AN: 68034

Other (OTH) AF: 0.976 AC: 2065 AN: 2116

Alfa AF: 0.972 Hom.: 10516

Bravo AF: 0.974

Asia WGS AF: 0.992 AC: 3450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.45
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs4650707; hg19: chr1-175122566;