rs4803178

chr19-53748783-A-G

Variant summary

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

The ENST00000710708.1(ENSG00000269842):n.1151+393A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 517,648 control chromosomes in the GnomAD database, including 435 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 0.034 (110 hom., cov: 32)
  • Exomes 𝑓: 0.037 (325 hom.)
• Consequence: ENST00000710708.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904765	XR_007067334.1	n.939+393A>G		intron_variant, non_coding_transcript_variant
LOC124904765	XR_007067333.1	n.847+393A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710708.1	n.1151+393A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0344 AC: 5239 AN: 152124 Hom.: 110 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0432

Gnomad OTH AF: 0.0440

GnomAD4 exome AF: 0.0375 AC: 13687 AN: 365406 Hom.: 325 AF XY: 0.0360 AC XY: 7502 AN XY: 208434

Gnomad4 AFR exome AF: 0.0127

Gnomad4 AMR exome AF: 0.0434

Gnomad4 ASJ exome AF: 0.0650

Gnomad4 EAS exome AF: 0.000154

Gnomad4 SAS exome AF: 0.0206

Gnomad4 FIN exome AF: 0.0336

Gnomad4 NFE exome AF: 0.0448

Gnomad4 OTH exome AF: 0.0409

GnomAD4 genome AF: 0.0345 AC: 5247 AN: 152242 Hom.: 110 Cov.: 32 AF XY: 0.0334 AC XY: 2488 AN XY: 74416

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.0553

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0432

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0383 Hom.: 33

Bravo AF: 0.0357

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	2.1
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4803178; hg19: chr19-54252037;