rs1961901

chr14-106680856-G-T

Variant summary

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

The ENST00000519713.1(IGHV1-67):n.104C>A 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 0.145 in 768,722 control chromosomes in the GnomAD database, including 9,090 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 (2752 hom., cov: 32)
  • Exomes 𝑓: 0.14 (6338 hom.)
• Consequence: IGHV1-67 ENST00000519713.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 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.104C>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26920 AN: 151960 Hom.: 2737 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.137 AC: 84718 AN: 616648 Hom.: 6338 Cov.: 0 AF XY: 0.137 AC XY: 45911 AN XY: 335928

Gnomad4 AFR exome AF: 0.283

Gnomad4 AMR exome AF: 0.148

Gnomad4 ASJ exome AF: 0.184

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.139

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.126

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.177 AC: 26969 AN: 152074 Hom.: 2752 Cov.: 32 AF XY: 0.177 AC XY: 13128 AN XY: 74326

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.187

Alfa AF: 0.156 Hom.: 266

Bravo AF: 0.186

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.0
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: rs1961901; hg19: chr14-107136873; COSMIC: COSV69868636;