4-76846492-C-T

Variant names:

• chr4-76846492-C-T
• rs1994854
• XM_047416557.1:c.145-1730C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC124900866 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.208 AC: 8606 AN: 41436

American (AMR) AF: 0.130 AC: 1978 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.109 AC: 565 AN: 5182

South Asian (SAS) AF: 0.249 AC: 1202 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1304 AN: 10558

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11688 AN: 67992

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.174 Hom.: 3466

Bravo AF: 0.178

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.41
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1994854; hg19: chr4-77767645;