chr14-106865837-T-C

Variant names:

• chr14-106865837-T-C
• rs885883
• unassigned_transcript_2645:c.59A>G

Variant summary

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

The ENST00000000000(IGHVII-78-1):​c.59A>G​(p.His20Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 162,890 control chromosomes in the GnomAD database, including 10,710 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 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 0.32 (9630 hom., cov: 32)
  • Exomes 𝑓: 0.40 (1080 hom.)
• Consequence: IGHVII-78-1 ENST00000000000 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 10 publications found

Genes affected

IGHVII-78-1 (HGNC:5691): (immunoglobulin heavy variable (II)-78-1 (pseudogene))

LOC124903399 (HGNC:):

IGH (HGNC:5477):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521105.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGHVII-78-1	ENST00000521105.1	TSL:6	n.59A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48611 AN: 151116 Hom.: 9633 Cov.: 32

Gnomad AFR AF: 0.0758

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.403 AC: 4692 AN: 11656 Hom.: 1080 Cov.: 0 AF XY: 0.399 AC XY: 2923 AN XY: 7330

African (AFR) AF: 0.0829 AC: 32 AN: 386

American (AMR) AF: 0.484 AC: 303 AN: 626

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 84 AN: 246

East Asian (EAS) AF: 0.479 AC: 315 AN: 658

South Asian (SAS) AF: 0.318 AC: 193 AN: 606

European-Finnish (FIN) AF: 0.472 AC: 795 AN: 1684

Middle Eastern (MID) AF: 0.351 AC: 283 AN: 806

European-Non Finnish (NFE) AF: 0.409 AC: 2469 AN: 6044

Other (OTH) AF: 0.363 AC: 218 AN: 600

GnomAD4 genome AF: 0.321 AC: 48611 AN: 151234 Hom.: 9630 Cov.: 32 AF XY: 0.327 AC XY: 24184 AN XY: 73904

African (AFR) AF: 0.0756 AC: 3129 AN: 41398

American (AMR) AF: 0.447 AC: 6799 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1272 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2354 AN: 5160

South Asian (SAS) AF: 0.377 AC: 1818 AN: 4824

European-Finnish (FIN) AF: 0.473 AC: 4955 AN: 10486

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27078 AN: 67378

Other (OTH) AF: 0.352 AC: 740 AN: 2100

Alfa AF: 0.382 Hom.: 50058

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs885883; hg19: chr14-107274052;