rs1051112

Variant names:

• chr14-105769274-A-C
• rs1051112
• ENST00000641136.1:c.1094T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-105769274-A-C
• chr14-105769274-A-G
• chr14-105769274-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000641136.1(IGHG3):​c.1094T>G​(p.Phe365Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000071 (0 hom., cov: 30)
  • Exomes 𝑓: 0.0000032 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IGHG3 ENST00000641136.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 6 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGHG3	unassigned_transcript_2476	c.1094T>G	p.Phe365Cys	missense_variant	Exon 7 of 9
IGHG3	unassigned_transcript_2477	c.1094T>G	p.Phe365Cys	missense_variant	Exon 7 of 7
IGH		n.105769274A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGHG3	ENST00000641136.1	c.1094T>G	p.Phe365Cys	missense_variant	Exon 7 of 9			ENSP00000492969.1
IGHG3	ENST00000390551.6	c.1094T>G	p.Phe365Cys	missense_variant	Exon 7 of 7	6		ENSP00000374993.2

Frequencies

GnomAD3 genomes AF: 0.00000713 AC: 1 AN: 140172 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000152

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000319 AC: 2 AN: 626520 Hom.: 0 Cov.: 0 AF XY: 0.00000586 AC XY: 2 AN XY: 341458

African (AFR) AF: 0.00 AC: 0 AN: 17314

American (AMR) AF: 0.00 AC: 0 AN: 43672

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20888

East Asian (EAS) AF: 0.00 AC: 0 AN: 36054

South Asian (SAS) AF: 0.00 AC: 0 AN: 69718

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53116

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3540

European-Non Finnish (NFE) AF: 0.00000286 AC: 1 AN: 349368

Other (OTH) AF: 0.0000304 AC: 1 AN: 32850

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000713 AC: 1 AN: 140172 Hom.: 0 Cov.: 30 AF XY: 0.0000146 AC XY: 1 AN XY: 68328

African (AFR) AF: 0.00 AC: 0 AN: 34344

American (AMR) AF: 0.00 AC: 0 AN: 14312

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3344

East Asian (EAS) AF: 0.00 AC: 0 AN: 4620

South Asian (SAS) AF: 0.00 AC: 0 AN: 4420

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10238

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 196

European-Non Finnish (NFE) AF: 0.0000152 AC: 1 AN: 65904

Other (OTH) AF: 0.00 AC: 0 AN: 1926

Alfa AF: 0.00 Hom.: 569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	21
DANN	Benign	0.84
PhyloP100		-0.035

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1051112; hg19: chr14-106235611;