chr4-105140377-C-A

Variant names:

• chr4-105140377-C-A
• rs7679673
• XM_047416559.1:c.*779-2659G>T

Variant summary

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

The ENST00000504082.1(ENSG00000251259):​n.110+133G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 152,018 control chromosomes in the GnomAD database, including 20,408 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 0.51 (20408 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000251259 ENST00000504082.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 140 publications found

Genes affected

LOC124900868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504082.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251259	ENST00000504082.1	TSL:4	n.110+133G>T		intron	N/A
	ENSG00000251259	ENST00000776606.1		n.149-2659G>T		intron	N/A
	ENSG00000251259	ENST00000776607.1		n.371-2659G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76970 AN: 151900 Hom.: 20369 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.507 AC: 77071 AN: 152018 Hom.: 20408 Cov.: 32 AF XY: 0.519 AC XY: 38533 AN XY: 74304

African (AFR) AF: 0.619 AC: 25678 AN: 41456

American (AMR) AF: 0.512 AC: 7815 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3466

East Asian (EAS) AF: 0.801 AC: 4143 AN: 5170

South Asian (SAS) AF: 0.585 AC: 2823 AN: 4828

European-Finnish (FIN) AF: 0.531 AC: 5621 AN: 10584

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27662 AN: 67934

Other (OTH) AF: 0.510 AC: 1078 AN: 2112

Alfa AF: 0.440 Hom.: 51193

Bravo AF: 0.510

Asia WGS AF: 0.681 AC: 2361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.82
DANN	Benign	0.30
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs7679673; hg19: chr4-106061534;