19-35433855-C-T

Variant names:

• chr19-35433855-C-T
• rs2312305
• ENST00000716259.1:n.260G>A

Variant summary

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

The ENST00000716259.1(ENSG00000288731):​n.260G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,156 control chromosomes in the GnomAD database, including 5,881 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 0.27 (5877 hom., cov: 32)
  • Exomes 𝑓: 0.48 (4 hom.)
• Consequence: ENSG00000288731 ENST00000716259.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 4 publications found

Genes affected

ENSG00000288731 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716259.1. 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
	LOC101927522	NR_187751.1		n.335-17G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288731	ENST00000716259.1		n.260G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000288731	ENST00000786314.1		n.259G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000288731	ENST00000786318.1		n.814G>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41358 AN: 151994 Hom.: 5867 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.477 AC: 21 AN: 44 Hom.: 4 Cov.: 0 AF XY: 0.500 AC XY: 15 AN XY: 30

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.475 AC: 19 AN: 40

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.272 AC: 41412 AN: 152112 Hom.: 5877 Cov.: 32 AF XY: 0.275 AC XY: 20444 AN XY: 74356

African (AFR) AF: 0.205 AC: 8493 AN: 41516

American (AMR) AF: 0.323 AC: 4943 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1837 AN: 5160

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4824

European-Finnish (FIN) AF: 0.310 AC: 3273 AN: 10558

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19223 AN: 67982

Other (OTH) AF: 0.274 AC: 579 AN: 2114

Alfa AF: 0.267 Hom.: 3886

Bravo AF: 0.269

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2312305;

hg19: chr19-35924757;