chr20-40632414-A-G

Variant names:

• chr20-40632414-A-G
• rs6072081
• XR_001754596.2:n.243+3174T>C

Variant summary

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

The XR_001754596.2(LOC102724968):​n.243+3174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,938 control chromosomes in the GnomAD database, including 19,096 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 0.49 (19096 hom., cov: 32)
• Consequence: LOC102724968 XR_001754596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 24 publications found

Genes affected

LOC102724968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74460 AN: 151820 Hom.: 19101 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.490 AC: 74464 AN: 151938 Hom.: 19096 Cov.: 32 AF XY: 0.491 AC XY: 36460 AN XY: 74244

African (AFR) AF: 0.329 AC: 13610 AN: 41412

American (AMR) AF: 0.492 AC: 7513 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2236 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2187 AN: 5152

South Asian (SAS) AF: 0.419 AC: 2023 AN: 4826

European-Finnish (FIN) AF: 0.589 AC: 6217 AN: 10550

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39091 AN: 67954

Other (OTH) AF: 0.467 AC: 983 AN: 2104

Alfa AF: 0.547 Hom.: 100973

Bravo AF: 0.478

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.27
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6072081; hg19: chr20-39261054;