19-28645675-T-C

Position:

• chr19-28645675-T-C

Variant summary

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

The NR_110759.1(LOC100420587):​n.656+76895A>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 0.341 in 152,118 control chromosomes in the GnomAD database, including 11,003 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 0.34 (11003 hom., cov: 33)
• Consequence: LOC100420587 NR_110759.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100420587	NR_110759.1	n.656+76895A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000585394.1	n.20+2609A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51768 AN: 152000 Hom.: 10964 Cov.: 33

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.341 AC: 51862 AN: 152118 Hom.: 11003 Cov.: 33 AF XY: 0.338 AC XY: 25110 AN XY: 74370

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.343

Alfa AF: 0.231 Hom.: 4942

Bravo AF: 0.357

Asia WGS AF: 0.304 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10401833; hg19: chr19-29136582;