5-76978712-T-C

Position:

• chr5-76978712-T-C

Variant summary

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

The ENST00000514258.1(CRHBP):​n.467+2192T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 152,050 control chromosomes in the GnomAD database, including 17,740 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 0.46 (17740 hom., cov: 32)
• Consequence: CRHBP ENST00000514258.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

CRHBP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRHBP	XR_948235.4	n.1057+2192T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRHBP	ENST00000514258.1	n.467+2192T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69491 AN: 151932 Hom.: 17706 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.458 AC: 69572 AN: 152050 Hom.: 17740 Cov.: 32 AF XY: 0.459 AC XY: 34092 AN XY: 74328

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.460

Alfa AF: 0.362 Hom.: 21393

Bravo AF: 0.462

Asia WGS AF: 0.513 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1715747; hg19: chr5-76274537;