rs17112078

Positions:

• chr14-106823737-A-G

Variant summary

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

The ENST00000523951.1(IGHV3-75):​n.308T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 160,244 control chromosomes in the GnomAD database, including 13,399 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 0.40 (12789 hom., cov: 32)
  • Exomes 𝑓: 0.36 (610 hom.)
• Consequence: IGHV3-75 ENST00000523951.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

IGHV3-75 (HGNC:5625): (immunoglobulin heavy variable 3-75 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGHV3-75	ENST00000523951.1	n.308T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60710 AN: 151818 Hom.: 12755 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.364 AC: 3023 AN: 8306 Hom.: 610 Cov.: 0 AF XY: 0.369 AC XY: 1668 AN XY: 4524

Gnomad4 AFR exome AF: 0.560

Gnomad4 AMR exome AF: 0.269

Gnomad4 ASJ exome AF: 0.362

Gnomad4 EAS exome AF: 0.309

Gnomad4 SAS exome AF: 0.420

Gnomad4 FIN exome AF: 0.359

Gnomad4 NFE exome AF: 0.366

Gnomad4 OTH exome AF: 0.347

GnomAD4 genome AF: 0.400 AC: 60803 AN: 151938 Hom.: 12789 Cov.: 32 AF XY: 0.401 AC XY: 29765 AN XY: 74264

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.334

Alfa AF: 0.356 Hom.: 18381

Bravo AF: 0.400

Asia WGS AF: 0.371 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17112078; hg19: chr14-107231967;