rs11085749

Positions:

• chr19-10850597-G-A

Variant summary

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

The NM_001136482.3(C19orf38):​c.340+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,547,716 control chromosomes in the GnomAD database, including 114,990 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 0.36 (10235 hom., cov: 31)
  • Exomes 𝑓: 0.39 (104755 hom.)
• Consequence: C19orf38 NM_001136482.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

C19orf38 (HGNC:34073): (chromosome 19 open reading frame 38) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C19orf38	NM_001136482.3	c.340+30G>A		intron_variant		ENST00000397820.5
C19orf38	XM_005259846.6	c.340+30G>A		intron_variant
C19orf38	XM_005259847.6	c.340+30G>A		intron_variant
C19orf38	XM_047438562.1	c.31+2058G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C19orf38	ENST00000397820.5	c.340+30G>A		intron_variant		1	NM_001136482.3	P1
C19orf38	ENST00000592854.5	c.340+30G>A		intron_variant		5		P1
C19orf38	ENST00000587494.1	n.354+30G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55294 AN: 151674 Hom.: 10202 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.359

GnomAD3 exomes AF: 0.377 AC: 57245 AN: 151706 Hom.: 11081 AF XY: 0.381 AC XY: 30792 AN XY: 80716

Gnomad AFR exome AF: 0.328

Gnomad AMR exome AF: 0.294

Gnomad ASJ exome AF: 0.352

Gnomad EAS exome AF: 0.534

Gnomad SAS exome AF: 0.389

Gnomad FIN exome AF: 0.408

Gnomad NFE exome AF: 0.380

Gnomad OTH exome AF: 0.391

GnomAD4 exome AF: 0.385 AC: 537855 AN: 1395924 Hom.: 104755 Cov.: 33 AF XY: 0.385 AC XY: 265398 AN XY: 688654

Gnomad4 AFR exome AF: 0.326

Gnomad4 AMR exome AF: 0.297

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.565

Gnomad4 SAS exome AF: 0.383

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.384

Gnomad4 OTH exome AF: 0.386

GnomAD4 genome AF: 0.365 AC: 55373 AN: 151792 Hom.: 10235 Cov.: 31 AF XY: 0.367 AC XY: 27213 AN XY: 74152

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.359

Alfa AF: 0.370 Hom.: 6383

Bravo AF: 0.359

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.25
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs11085749; hg19: chr19-10961273; COSMIC: COSV67318415;