rs669764

Variant names:

• chr1-78225976-C-T
• rs669764
• ENST00000823881.1:n.203+573C>T

Variant summary

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

The ENST00000823881.1(MGC27382):​n.203+573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,784 control chromosomes in the GnomAD database, including 15,408 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 0.43 (15408 hom., cov: 32)
• Consequence: MGC27382 ENST00000823881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 5 publications found

Genes affected

MGC27382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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
MGC27382	ENST00000823881.1	n.203+573C>T		intron_variant	Intron 2 of 3
MGC27382	ENST00000823882.1	n.172+573C>T		intron_variant	Intron 2 of 3
MGC27382	ENST00000823883.1	n.230+573C>T		intron_variant	Intron 2 of 2
MGC27382	ENST00000823884.1	n.182+573C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65360 AN: 151664 Hom.: 15383 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.431 AC: 65436 AN: 151784 Hom.: 15408 Cov.: 32 AF XY: 0.436 AC XY: 32306 AN XY: 74166

African (AFR) AF: 0.608 AC: 25144 AN: 41376

American (AMR) AF: 0.411 AC: 6272 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3564 AN: 5122

South Asian (SAS) AF: 0.357 AC: 1718 AN: 4816

European-Finnish (FIN) AF: 0.403 AC: 4237 AN: 10522

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.322 AC: 21901 AN: 67926

Other (OTH) AF: 0.432 AC: 910 AN: 2108

Alfa AF: 0.360 Hom.: 44240

Bravo AF: 0.444

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs669764; hg19: chr1-78691660;