chr19-22032639-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 106 publications found

Genes affected

ENSG00000269504 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670990.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000269504	ENST00000596778.1	TSL:1	n.506+2034T>C		intron	N/A
	ENSG00000269504	ENST00000670990.1		n.994T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000269504	ENST00000651236.1		n.1244-548T>C		intron	N/A

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

African (AFR) AF: 0.477 AC: 19764 AN: 41464

American (AMR) AF: 0.357 AC: 5449 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1684 AN: 5136

South Asian (SAS) AF: 0.380 AC: 1836 AN: 4830

European-Finnish (FIN) AF: 0.308 AC: 3250 AN: 10540

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19578 AN: 67950

Other (OTH) AF: 0.322 AC: 681 AN: 2114

Alfa AF: 0.329 Hom.: 1555

Bravo AF: 0.357

Asia WGS AF: 0.328 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.10
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: rs8105767;

hg19: chr19-22215441;