19-22032639-A-G

Variant names:

• chr19-22032639-A-G
• rs8105767
• ENST00000596778.1:n.506+2034T>C

Variant summary

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

The ENST00000670990.1(ENSG00000269504):​n.994T>C 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 0.354 in 151,982 control chromosomes in the GnomAD database, including 10,009 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 0.35 (10009 hom., cov: 33)
• Consequence: ENSG00000269504 ENST00000670990.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

ENSG00000269504 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268248	XR_002958429.1	n.1952-548T>C		intron_variant	Intron 10 of 14
LOC112268248	XR_007067184.1	n.1951+2034T>C		intron_variant	Intron 10 of 12
LOC112268248	XR_007067185.1	n.1446+2034T>C		intron_variant	Intron 11 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269504	ENST00000596778.1	n.506+2034T>C		intron_variant	Intron 4 of 8	1
ENSG00000269504	ENST00000670990.1	n.994T>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000269504	ENST00000651236.1	n.1244-548T>C		intron_variant	Intron 10 of 13

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53662 AN: 151864 Hom.: 9975 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.354 AC: 53754 AN: 151982 Hom.: 10009 Cov.: 33 AF XY: 0.355 AC XY: 26350 AN XY: 74270

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.322

Alfa AF: 0.325 Hom.: 1464

Bravo AF: 0.357

Asia WGS AF: 0.328 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8105767; hg19: chr19-22215441;