chr10-21744013-A-G

Variant names:

• chr10-21744013-A-G
• rs7072776
• XR_001747388.2:n.3189+6427T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001747388.2(LOC107984214):​n.3189+6427T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,102 control chromosomes in the GnomAD database, including 33,762 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 0.66 (33762 hom., cov: 32)
• Consequence: LOC107984214 XR_001747388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

Genes affected

LOC107984214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984214	XR_001747388.2	n.3189+6427T>C		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99652 AN: 151984 Hom.: 33765 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.655 AC: 99666 AN: 152102 Hom.: 33762 Cov.: 32 AF XY: 0.661 AC XY: 49168 AN XY: 74346

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.629

Alfa AF: 0.697 Hom.: 54383

Bravo AF: 0.640

Asia WGS AF: 0.790 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7072776; hg19: chr10-22032942;