rs62092220

Variant names:

• chr18-22148845-C-A
• rs62092220
• ENST00000780840.1:n.137+19466G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-22148845-C-A
• chr18-22148845-C-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000780840.1(GATA6-AS1):​n.137+19466G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,076 control chromosomes in the GnomAD database, including 3,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (3204 hom., cov: 32)
• Consequence: GATA6-AS1 ENST00000780840.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.166
• Publications: 0 publications found

Genes affected

GATA6-AS1 (HGNC:48840): (GATA6 antisense RNA 1 (head to head))

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 18-22148845-C-A is Benign according to our data. Variant chr18-22148845-C-A is described in ClinVar as Benign. ClinVar VariationId is 873213.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780840.1. 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
	GATA6-AS1	ENST00000780840.1		n.137+19466G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27188 AN: 151958 Hom.: 3202 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.179 AC: 27188 AN: 152076 Hom.: 3204 Cov.: 32 AF XY: 0.177 AC XY: 13142 AN XY: 74330

African (AFR) AF: 0.0505 AC: 2096 AN: 41544

American (AMR) AF: 0.132 AC: 2018 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5184

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4812

European-Finnish (FIN) AF: 0.242 AC: 2548 AN: 10550

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18046 AN: 67920

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.142 Hom.: 390

Bravo AF: 0.163

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs62092220; hg19: chr18-19728806;