14-106823737-A-G

Variant names:

• chr14-106823737-A-G
• rs17112078
• unassigned_transcript_2639:c.307T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000000000(IGHV3-75):​c.307T>C​(p.Leu103Leu) variant causes a synonymous 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 ENST00000000000 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 6 publications found

Genes affected

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

IGH (HGNC:5477):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=0.072 with no splicing effect.
• 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 rank	MANE	Protein	UniProt
IGHV3-75	unassigned_transcript_2639	c.307T>C	p.Leu103Leu	synonymous_variant	Exon 2 of 2
IGH		n.106823737A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGHV3-75	ENST00000523951.1	n.308T>C		non_coding_transcript_exon_variant	Exon 2 of 2	6

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

African (AFR) AF: 0.560 AC: 84 AN: 150

American (AMR) AF: 0.269 AC: 49 AN: 182

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 21 AN: 58

East Asian (EAS) AF: 0.309 AC: 60 AN: 194

South Asian (SAS) AF: 0.420 AC: 147 AN: 350

European-Finnish (FIN) AF: 0.359 AC: 1715 AN: 4778

Middle Eastern (MID) AF: 0.392 AC: 29 AN: 74

European-Non Finnish (NFE) AF: 0.366 AC: 818 AN: 2232

Other (OTH) AF: 0.347 AC: 100 AN: 288

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

African (AFR) AF: 0.535 AC: 22170 AN: 41408

American (AMR) AF: 0.328 AC: 5005 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1529 AN: 5166

South Asian (SAS) AF: 0.408 AC: 1962 AN: 4810

European-Finnish (FIN) AF: 0.370 AC: 3907 AN: 10558

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23707 AN: 67932

Other (OTH) AF: 0.334 AC: 707 AN: 2114

Alfa AF: 0.366 Hom.: 44582

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
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs17112078; hg19: chr14-107231967;