chr5-41579023-G-A

Variant names:

• chr5-41579023-G-A
• rs607145
• ENST00000742936.1:n.104+1566G>A

Variant summary

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

The ENST00000742936.1(ENSG00000296840):​n.104+1566G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,220 control chromosomes in the GnomAD database, including 965 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 0.10 (965 hom., cov: 32)
• Consequence: ENSG00000296840 ENST00000742936.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.601
• Publications: 3 publications found

Genes affected

ENSG00000296840 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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
ENSG00000296840	ENST00000742936.1	n.104+1566G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15662 AN: 152102 Hom.: 963 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0638

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.103 AC: 15665 AN: 152220 Hom.: 965 Cov.: 32 AF XY: 0.100 AC XY: 7452 AN XY: 74416

African (AFR) AF: 0.178 AC: 7376 AN: 41534

American (AMR) AF: 0.0842 AC: 1288 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3468

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5176

South Asian (SAS) AF: 0.0630 AC: 304 AN: 4826

European-Finnish (FIN) AF: 0.0471 AC: 499 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0802 AC: 5454 AN: 67994

Other (OTH) AF: 0.108 AC: 229 AN: 2114

Alfa AF: 0.0900 Hom.: 406

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs607145; hg19: chr5-41579125;