rs2011167

chr14-106680831-A-G

Variant summary

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

The ENST00000519713.1(IGHV1-67):n.129T>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 0.135 in 770,484 control chromosomes in the GnomAD database, including 7,335 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 0.15 (1686 hom., cov: 32)
  • Exomes 𝑓: 0.13 (5649 hom.)
• Consequence: IGHV1-67 ENST00000519713.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824

Genes affected

IGHV1-67 (HGNC:5556): (immunoglobulin heavy variable 1-67 (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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
IGHV1-67	ENST00000519713.1	n.129T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22125 AN: 152040 Hom.: 1679 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.132 AC: 81496 AN: 618330 Hom.: 5649 Cov.: 0 AF XY: 0.132 AC XY: 44504 AN XY: 336996

Gnomad4 AFR exome AF: 0.175

Gnomad4 AMR exome AF: 0.140

Gnomad4 ASJ exome AF: 0.152

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.139

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.142

GnomAD4 genome AF: 0.146 AC: 22153 AN: 152154 Hom.: 1686 Cov.: 32 AF XY: 0.146 AC XY: 10862 AN XY: 74372

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.164

Alfa AF: 0.136 Hom.: 180

Bravo AF: 0.150

Asia WGS AF: 0.139 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	3.2
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2011167; hg19: chr14-107136848; COSMIC: COSV69868635;