chr4-76846492-C-T

Position:

• chr4-76846492-C-T

Variant summary

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

The XM_047416557.1(LOC124900866):​c.145-1730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,030 control chromosomes in the GnomAD database, including 2,527 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 0.18 (2527 hom., cov: 32)
• Consequence: LOC124900866 XM_047416557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

Genes affected

LOC124900866 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900866	XM_047416557.1	c.145-1730C>T		intron_variant			XP_047272513.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26771 AN: 151912 Hom.: 2511 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.176 AC: 26818 AN: 152030 Hom.: 2527 Cov.: 32 AF XY: 0.175 AC XY: 12995 AN XY: 74294

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.185

Alfa AF: 0.173 Hom.: 2724

Bravo AF: 0.178

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1994854; hg19: chr4-77767645;