chr5-42405409-G-A

Variant names:

• chr5-42405409-G-A
• rs2940930
• ENST00000820257.1:n.347+5643G>A

Variant summary

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

The ENST00000820257.1(ENSG00000306695):​n.347+5643G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,332 control chromosomes in the GnomAD database, including 8,716 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 0.32 (8716 hom., cov: 32)
• Consequence: ENSG00000306695 ENST00000820257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 4 publications found

Genes affected

ENSG00000306695 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 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
ENSG00000306695	ENST00000820257.1	n.347+5643G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.324 AC: 48955 AN: 151218 Hom.: 8719 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.324 AC: 48973 AN: 151332 Hom.: 8716 Cov.: 32 AF XY: 0.329 AC XY: 24293 AN XY: 73892

African (AFR) AF: 0.184 AC: 7580 AN: 41268

American (AMR) AF: 0.367 AC: 5575 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1235 AN: 3460

East Asian (EAS) AF: 0.544 AC: 2802 AN: 5150

South Asian (SAS) AF: 0.487 AC: 2343 AN: 4812

European-Finnish (FIN) AF: 0.371 AC: 3854 AN: 10400

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24611 AN: 67738

Other (OTH) AF: 0.310 AC: 651 AN: 2102

Alfa AF: 0.360 Hom.: 5262

Bravo AF: 0.315

Asia WGS AF: 0.483 AC: 1667 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.051
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2940930; hg19: chr5-42405511;