rs1145603

Variant names:

• chr5-157861421-G-A
• rs1145603
• ENST00000734152.1:n.283G>A

Variant summary

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

The ENST00000734152.1(ENSG00000295935):​n.283G>A 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 0.597 in 152,082 control chromosomes in the GnomAD database, including 27,577 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 0.60 (27577 hom., cov: 32)
• Consequence: ENSG00000295935 ENST00000734152.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 0 publications found

Genes affected

ENSG00000295935 (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 = 0.684 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
ENSG00000295935	ENST00000734152.1	n.283G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90665 AN: 151964 Hom.: 27533 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.597 AC: 90761 AN: 152082 Hom.: 27577 Cov.: 32 AF XY: 0.599 AC XY: 44511 AN XY: 74336

African (AFR) AF: 0.690 AC: 28628 AN: 41468

American (AMR) AF: 0.464 AC: 7097 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2146 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2070 AN: 5170

South Asian (SAS) AF: 0.600 AC: 2896 AN: 4830

European-Finnish (FIN) AF: 0.676 AC: 7146 AN: 10572

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38927 AN: 67968

Other (OTH) AF: 0.586 AC: 1237 AN: 2112

Alfa AF: 0.602 Hom.: 4150

Bravo AF: 0.578

Asia WGS AF: 0.505 AC: 1757 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	11
DANN	Benign	0.61
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1145603; hg19: chr5-157288429;