20-40632414-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC102724968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724968	XR_001754596.2	n.243+3174T>C		intron_variant	Intron 3 of 7
LOC102724968	XR_001754597.1	n.180+11497T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.467

Alfa AF: 0.557 Hom.: 47585

Bravo AF: 0.478

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6072081; hg19: chr20-39261054;