19-50837750-G-C

Variant names:

• chr19-50837750-G-C
• rs35711205
• ENST00000598079.1:n.213+6457G>C

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.213+6457G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,978 control chromosomes in the GnomAD database, including 4,024 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 0.23 (4024 hom., cov: 31)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733
• Publications: 6 publications found

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598079.1. 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
	LOC105372441	NR_131203.1		n.213+6457G>C		intron	N/A
	LOC105372441	NR_131205.1		n.230+6457G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267968	ENST00000598079.1	TSL:3	n.213+6457G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34574 AN: 151860 Hom.: 4029 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.228 AC: 34581 AN: 151978 Hom.: 4024 Cov.: 31 AF XY: 0.233 AC XY: 17291 AN XY: 74256

African (AFR) AF: 0.265 AC: 10970 AN: 41434

American (AMR) AF: 0.191 AC: 2912 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 876 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1135 AN: 5152

South Asian (SAS) AF: 0.150 AC: 723 AN: 4814

European-Finnish (FIN) AF: 0.310 AC: 3276 AN: 10556

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13953 AN: 67962

Other (OTH) AF: 0.232 AC: 489 AN: 2112

Alfa AF: 0.0909 Hom.: 121

Bravo AF: 0.222

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.67
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs35711205; hg19: chr19-51341006;