rs11672183

chr19-53676948-C-T

Variant summary

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

The ENST00000710708.1(ENSG00000269842):n.349-13345C>T 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 0.0582 in 152,236 control chromosomes in the GnomAD database, including 320 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 0.058 (320 hom., cov: 32)
• Consequence: ENST00000710708.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985342	XR_007067332.1	n.356-17081C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710708.1	n.349-13345C>T		intron_variant, non_coding_transcript_variant
	ENST00000710710.1	n.167-1427C>T		intron_variant, non_coding_transcript_variant
	ENST00000710735.1	n.166-1427C>T		intron_variant, non_coding_transcript_variant
	ENST00000710736.1	n.37-10938C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0582 AC: 8853 AN: 152118 Hom.: 319 Cov.: 32

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0582 AC: 8861 AN: 152236 Hom.: 320 Cov.: 32 AF XY: 0.0601 AC XY: 4474 AN XY: 74424

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.0652

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0509

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.0583

Alfa AF: 0.0548 Hom.: 52

Bravo AF: 0.0595

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.63
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11672183; hg19: chr19-54180202;