rs34295723

Variant names:

• chr14-105766769-G-A
• rs34295723
• ENST00000641136.1:c.1255-772C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-105766769-G-A
• chr14-105766769-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641136.1(IGHG3):​c.1255-772C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 139,360 control chromosomes in the GnomAD database, including 20,164 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 0.51 (20164 hom., cov: 22)
• Consequence: IGHG3 ENST00000641136.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 1 publications found

Genes affected

IGHG3 (HGNC:5527): (immunoglobulin heavy constant gamma 3 (G3m marker)) Predicted to enable antigen binding activity and immunoglobulin receptor binding activity. Involved in retina homeostasis. Located in blood microparticle and extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

IGH (HGNC:5477):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641136.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGHG3	ENST00000641136.1		c.1255-772C>T		intron	N/A	ENSP00000492969.1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 71247 AN: 139242 Hom.: 20169 Cov.: 22

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.511 AC: 71258 AN: 139360 Hom.: 20164 Cov.: 22 AF XY: 0.502 AC XY: 33914 AN XY: 67622

African (AFR) AF: 0.260 AC: 9915 AN: 38088

American (AMR) AF: 0.420 AC: 5738 AN: 13658

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2539 AN: 3266

East Asian (EAS) AF: 0.0882 AC: 384 AN: 4356

South Asian (SAS) AF: 0.487 AC: 1899 AN: 3902

European-Finnish (FIN) AF: 0.576 AC: 5499 AN: 9546

Middle Eastern (MID) AF: 0.633 AC: 114 AN: 180

European-Non Finnish (NFE) AF: 0.685 AC: 43574 AN: 63652

Other (OTH) AF: 0.528 AC: 995 AN: 1886

Alfa AF: 0.579 Hom.: 2800

Asia WGS AF: 0.305 AC: 1057 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.40
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs34295723; hg19: chr14-106233106; COSMIC: COSV66653132;