rs7679673

Positions:

• chr4-105140377-C-A
• chr4-105140377-C-T

Variant summary

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

The XM_047416559.1(LOC124900868):​c.*779-2659G>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: LOC124900868 XM_047416559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

LOC124900868 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900868	XM_047416559.1	c.*779-2659G>T		intron_variant			XP_047272515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000504082.1	n.110+133G>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.510

Alfa AF: 0.431 Hom.: 19055

Bravo AF: 0.510

Asia WGS AF: 0.681 AC: 2361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7679673; hg19: chr4-106061534;